North Carolina Newborn Exome Sequencing for Universal Screening
Phase: NA
Conditions: Metabolism, Inborn Errors, Hearing Loss, Hereditary Disease
Sponsor: University of North Carolina, Chapel Hill

C o m pl et e Titl e: N C N E X U S: N ort h C ar oli n a N e w b or n E x o m e S e q u e nci n g f or U ni v ers al 
Scr e e ni n g   
  
  
  
 
S h ort Titl e:  N C N E X U S  
Dr u g or D e vic e N a m e(s):  N/ A 
F D A I N D/I D E (if a p plic a bl e):  I D E # G 1 5 0 2 5 8 
S p o ns or:  NI H  
Pr ot oc ol D at e:  0 6/ 1 8/ 2 0 1 3  
N C T N u m b er: N C T 0 2 8 2 6 6 9 4  
 
 
 
 
 
 
 
 
 
 
 
 
 
S p o ns or  
N ati o n al I nstit ut es of H e alt h  
9 0 0 0 R oc k vill e Pi k e  
B et h es d a, M aryl a n d 2 0 8 9 2  
U S A  
 
St u d y Pri nci p al I n v esti g at or C y nt hi a M. P o w ell, M D  
Di visi o n of P e di atric G e n etics a n d M et a b olis m  
M e dic al Sc h o ol Wi n g E  
C B # 7 4 8 7, U N C -C H  
C h a p el Hill, N C 2 7 5 9 9 -7 4 8 7  
P h o n e 9 1 9 -9 6 6 -4 2 0 2  
e m ail: p o w ellc m @ m e d. u nc. e d u  
 
 

1.  Cli ni c al  Pr ot o c ol  
 
Title of Cli nic al  Pr ot oc ol  
S h ort Na me:  T he N C N E X U S St u d y 
L o n g Na me: T he N ort h Car oli na Ne w b or n E x o me Se q ue nci n g f or U ni vers al Scree ni n g 
St u d y 
 
St u d y  D e si g n  
 
Ge ner al St u d y  Desi g n  
T he N C N E X U S pr oject is a n e x pl orat or y l o n git u di nal c o h ort st u d y, wit h ra n d o mizati o n 
of e nr olle d pare nts i nt o t w o gr o u ps wit h differe nt o p p ort u nities f or decisi o n- ma ki n g 
a b o ut cate g ori es of n o n- me dicall y acti o na ble g e n o mic i nf or mati o n.  
 
C o h ort s:  
We will e nr oll par e nts a n d t heir eli gi ble c hil d i nt o t he f oll o wi n g 2 c o h orts: 
 
T he “ Dia g n os e d C o h ort”: O ur g oal is t o se q ue nce 2 0 0 c hil dre n fr o m 
t his c o h ort i ncl u di n g i nfa nts a n d c hil dre n u p t o a g e 5 w h o ha ve 
meta b olic dis or ders s uc h as p he n yl ket o n uria ( P K U) a n d me di u m 
c hai n ac yl - C o A-de h y dr o ge nase deficie n c y ( M C A D D); c y stic fi br osis 
( C F) a n d C F T R -relate d meta b olic s y n dr o me ( C R M S); c o n ge nital 
heari n g l oss; pri mar y cili ar y d ys ki nesia, a n d a vari et y of ot her rare 
c o n diti o ns. 
 
T he “ Well - C hil d C o h ort”: O ur g oal is t o se q ue nce 2 0 0 i nfa nts w h ose 
pare nts e nr oll pre natall y. T he e x pecta nt m ot hers m ust be pre g na nt 
wit h a n i ntra uteri ne pre g na nc y of 1 8 w ee ks or greater, ha v e n o 
pe n di n g or p ositi ve pre natal dia g n ostic test res ults f or c o n ge nital 
malf or mati o ns or c hr o m os o mal a b n or malities a n d ha ve bee n i de ntifie d 
b y me dical pers o n n el i n t he o bstetrics cli nic as p ossi ble ca n di dates. 
 
We will c o nsi der r e q uests fr o m c o u ples w h o recei ve t heir O B care els e w here b ut 
w h o ha ve ha d c o ns ultati o ns wit h t he U N C pre natal cli nic o n a cas e- b y- case basis.   
 
 
R a n d o mi z ati o n:  
I n or der t o ass ess t he i m pact of t he a d diti o nal n o n- me dicall y acti o na ble g e n o mic fi n di n gs 
a vaila ble u p o n r e q uest, p are nts will be ra n d o mize d i n a 2: 1 rati o t o “ Decisi o n” or 
“ C o ntr ol” gr o u ps, res p ecti vel y. B ot h gr o u ps will lear n a n y c hil d h o o d o nset me dicall y 
acti o na ble r es ults (“ N G S -N B S ”) fr o m ge n o mic s e q ue nci n g at t heir ret ur n of res ult visit. 
 
St u d y d e si g n  n arr ati v e:  
 
T he N C N E X U S pr oject will utilize a s yste m of tiere d i nf or m e d c o nse nt b y w hic h  pare nts 
will partici pate i n a st u d y of i nf or me d decisi o n - ma ki n g a b o ut w het her t he y w o ul d acce pt 

N G S - N B S f or t heir c hil d or i nfa nt, a n d (i n t he cas e of t h ose ra n d o mize d t o t he 
“ Decisi o n” gr o u p) w h et her t he y wis h t o lear n a b o ut ot her a d diti o nal cate g ories of 
ge n o mic i nf or mati o n. 
 
P ote ntial partici pa nts will be a p pr oac he d b y a recr uiter d uri n g a re g ul arl y s c he d ule d 
cli nic visit a n d pr o vi de d wit h a n i nf or mati o nal br oc h ure a b o ut t he N C N E X U S st u d y 
( N E X U S Recr uit me nt Br oc h ure f or t he Dia g n os e d c o h ort: A p pe n di x 9 a n d N E X U S 
Recr uit me nt Br oc h ure f or t he Well -c hil d c o h ort: A p pe n di x 1 0). 
 
If t he y ar e i ntereste d i n lear ni n g m ore a b o ut t he st u d y, c o ntact 
i nf or mati o n will be o btai ne d a n d t he y will be gi ve n a st u d y br oc h ure 
a n d c o nse nt f or m. 
 
T here will be n o f urt her i nteracti o ns wit h pare nts w h o decli ne t o lear n m ore a b o ut 
t he st u d y 
Pare nts w h o e x presse d i ntere st i n t he st u d y will recei ve a t ele p h o ne 
call d uri n g w hic h t he i nf or me d c o nse nt f or i nitial partici pati o n will be 
re vie we d a n d c o ns e nt gi ve n ver ball y 
( N C N E X U S _i nf or mati o n _s heet _ P hase _I _ Di a g n ose d c o h ort: 
A p pe n di x 1 1 a n d N C N E X U S _i nf or mati o n _s heet _ P hase _I _ W C 
c o h ort: A p pe n di x 1 2). 
 
T h ose w h o a gree t o partici pate will be gi ve n access t o t he o nli ne 
decisi o n ai d, w hic h will pr o vi de i nf or mati o n a b o ut ge n o mic 
se q ue nci n g a n d t he p ot e ntial t y pes of res ults t hat w o ul d be i ncl u de d i n 
t he “ N G S-N B S” a n al ysis ( N C N E X U S Dec isi o n ai d o ver vie w: 
A p pe n di x 1 3; N E X U S O nli ne D A Decisi o n 1 S h o oti n g Scri pt: 
A p pe n di x 1 4; N E X U S O nli ne D A S h o oti n g Scri pt Q A c o nte nt: 
A p pe n di x 1 5). 
 
T h ose w h o are n ot i ntereste d i n partici pati n g will c o m plete a n e xit 
q uesti o n naire f or d ecli ners.  
 
After r ec ei vi n g a d diti o nal i nf or mati o n t hr o u g h t he electr o nic d ecisi o n ai d, pare nts w h o 
are i nter este d i n o btai ni n g se q ue nci n g f or t heir c hil d will be sc he d ule d f or a n i n- pers o n 
st u d y visit (“ Visit 1”) wit h a ge netic c o u nsel or t o o btai n f or mal c o nse nt f or se q ue nci n g 
( N C N E X U S _c o nse nt _ p hase II _ dia g n ose d c o h ort: A p pe n di x 1 6 a n d N C 
N E X U S _c o nse nt _ p has e II _ Well - C hil d c o h ort: A p pe n di x 1 7). C hee k s w a b sa m ples will 
be deli vere d t o t he B S P a n d M G L f or pr o cessi n g. E x o me se q ue nci n g will b e 
perf or me d, wit h f oc use d i nf or matics a nal ysis de pe n di n g o n t he c o h ort ( descri be d 
bel o w). 
 
T he ra n d o mizati o n stat us will be re veal e d t o t he p are nts w he n t h e y are sc h e d ule d f or t heir 
ret ur n of r es ults. Pare nts w h o are ra n d o mize d t o t h e “ decisi o n” gr o u p will be gi ve n access 
t o a d diti o nal c o nte nt i n t he electr o ni c decisi o n ai d pri or t o t heir sec o n d i n- p ers o n st u d y 
visit ( N E X U S _ O nli ne D A _ Decisi o n 2 _ S h o oti n g scri pt: A p pe n di x 1 8). T his i nf or mati o n 
will i ncl u de a descri pti o n of t he a d diti o nal cate g ories of n o n- me dicall y acti o na ble 

i nf or mati o n. 
 
C o u ples fr o m t he well-c hil d c o h ort w h o are ra n d o mize d t o t he c o ntr ol gr o u p a n d w h o 
ha ve ne g ati ve N G S - N B S res ults, ma y lear n t hes e res ults b y a sc he d ule d p h o ne call wit h a 
ge netic c o u nsel or/cli nical ge neticist.  
 
C o u ples fr o m t he well-c hil d c o h ort w h o are ra n d o mize d t o t he decisi o n gr o u p a n d are 
re q uesti n g res ults fr o m t he carrier stat us cate g or y will be a ble t o lear n t hes e res ults d uri n g 
a sc he d ule d p h o n e call wit h a ge netic c o u nsel or.  If t he y ha ve re q ueste d eit her or b ot h of 
t he ot her t w o cat e g ories of a d diti o nal i nf or mati o n a n d t hese are ne g ati ve, all of t heir 
a d diti o nal res ults ma y be discl ose d d uri n g a sc he d ule d p h o ne call wit h a g e netic 
c o u nsel or/cli nical ge n eticist.  
 
All partici pa nts wit h cli nicall y rele va nt p ositi ve res ults will   ha ve a sec o n d i n - pers o n 
st u d y visit (“ Visit 2”) wit h a b oar d certifie d me di cal ge neticist a n d ge n etic c o u nsel or f or 
ret ur n  of  r es ults  fr o m  N G S-N B S  a n d  (i n  t he  case  of  t h e  “ Dia g n os e d  C o h ort”)  t he  
i n dicati o n-base d a n al ysis , a n d f or t he ot her t w o a d diti o nal cate g ories of i nf or mati o n. 
 
Pa re nts w h o are ra n d o mi ze d t o t he “c o ntr ol” gr o u p will recei ve 
t heir pri mar y res ults b ut will n ot be eli gi ble f or a d diti o nal 
cate g ories of i nf or mati o n. 
 
Pare nts w h o are ra n d o mi ze d t o t he “ d ecisi o n” gr o u p will recei ve t heir 
pri mar y res ults a n d will ha ve t he o p p ort u nit y t o disc uss a n y q uesti o ns 
t he y ha ve re g ar di n g a d diti o nal cate g ories of n o n-me dicall y acti o na ble 
i nf or mati o n. T he y will t he n be eli gi ble t o re q u est a nal ysis of a n y, all, 
or n o ne of t he a d diti o nal i nf or mati o n. 
 
Pare nts ra n d o mize d t o t h e “ decisi o n” gr o u p will ha ve u p t o o ne a d diti o nal visit 
wit h a me dical ge n eticist a n d/ or ge netic c o u nsel or (“ Visit 3”) de p e n di n g o n t he 
a d diti o nal cate g ories of n o n- me dicall y acti o na bl e i nf or mati o n t he y ha ve 
re q ueste d. 
 
Pare nts will be as ke d t o c o m plete q uesti o n naires at defi ne d ti me p oi nts d uri n g t he 
st u d y (see st u d y desi g n sc he matic bel o w). Pare nts w h o c o m plete t he 
q uesti o n naires will be pai d $ 2 0 f or eac h q uesti o n naire c o m plete d. Pa y m e nt will 
be maile d i m me diatel y u p o n c o m pleti o n of a q uesti o n naire. We h a ve f o u n d t hat 
t his a m o u nt of m o ne y rec o g nizes t heir ti me a n d eff ort b ut is n ot c oerci ve. 
Meas ures i ncl u d e d i n t hese q uesti o n naires are s h o w n i n N C N E X U S Pr oject 3 
L o n git u di nal St u d y Meas ure (see A p pe n di x 1 9). Sli g ht c ha n ges or a dj ust me nts 
base d o n fee d bac k fr o m user testi n g ma y lea d t o mi n or c ha n ges (e. g., t o re d uce 
b ur de n b y re m o vi n g s o m e ite ms or meas ures, c ha n ge w or di n g if a n y is f o u n d t o 
be c o nf usi n g t o users, or a d d meas ures if users s u g gest we are missi n g a ke y 
c o nstr uct), i n w hic h case t he F D A will be pr o vi de d wi t h a 5- da y n otice of a n y 
u p dates or c h a n ges i n t he meas ures. 
 
I nt a ke F or m ( Dr aft v ersi o n will be pr o vi de d u p o n re q uest): T he 

i nta ke f or m c ollects i nf or mati o n a b o ut de m o gra p hics, pre vi o us 
e x perie n ce wit h ge n etic testi n g, k n o wle d ge a b o ut ge n o mic 
se q ue nci n g, a n d (f or t he “ Well - C hil d” C o h ort) pre g na nc y a n xiet y. 
Pare nts will be as ke d t o c o m plete t his f or m a n d bri n g it wit h t he m t o 
t he i nitial st u d y visit, if t he y a gree t o a visit.  
 
Ti m e 1 q uesti o n n aire ( Dr aft v ersi o n u p o n re q uest) : After p are nts 
deci de t o pr ocee d wit h a n i n- pers o n st u d y visit (eit her t o c o nse nt t o 
N G S - N G S or t o get m ore i nf or mati o n a b o ut it i n a n i n- pers o n 
c o ns ultati o n) or n ot t o pr ocee d wit h a n i n- p ers o n visit ( decli ni n g 
f urt her partici pati o n i n t he st u d y), t he y will be gi ve n access t o t he 
Ti me 1 q uesti o n naire, w hic h will pr o vi de val ua ble i nf or mati o n a b o ut 
differe n ces b et wee n p are nts w h o are a n d w h o are n ot i ntereste d i n  
N G S -N B S.  
 
Ti m e 2 q uesti o n n aire ( Dr aft v ersi o n will be pr o vi de d u p o n 
re q uest): All pare nts w h o atte n d t he i nitial i n- pers o n st u dy visit 
( w het her or n ot t he y ha v e acce pte d N G S-N B S) will c o m plete t he 
Ti me 2 q uesti o n naire, w hic h gat hers dat a a b o ut t heir decisi o n- ma ki n g 
pr ocess, m o o d, a n d k n o wle d ge a b o ut t he pr oject. I n a d diti o n, pare nts 
i n t he “ decisi o n” gr o u p will be as ke d t o c o m plete a brief p ost- 
decisi o n q uesti o n naire (t he Ti me 2 A q uesti o n naire) aft er t he y deci de 
w het her or n ot t o re q uest a d diti o nal ge n o mic fi n di n gs t o assess t he 
c o nse q ue nces of h a vi n g t his o pti o n. 
 
F oll o w u p Assess me nts ( Ti me 3 a n d Ti me 4 q uesti o n n aires) ( Dr aft 
ve rsi o ns will be pr o vi de d u p o n re q uest) : All pare nts will c o m plete 
t w o f oll o w u p q uesti o n naires f oll o wi n g t he ret ur n of res ult visit: a 
Ti me 3 q uesti o n naire c o m plete d wit hi n 2 wee ks of t he visit a n d a 
Ti me 4 q uesti o n naire c o m plete d 3 m o nt hs after t he visit. T hese 
q uesti o n naires will assess t he s h ort- a n d l o n ger-ter m c o nse q ue n ces of 
decisi o n - ma ki n g a n d res ults discl os ure. 
 
St u d y Desi g n Sc he m atic  Fi g ure  

 

 
 
 
2 
St u d y  Pr o c e d ur e s  
 
P artici p a nt  Selecti o n  
Partici pa nts ca n be eit her se x a n d of a n y race or et h nicit y, b ut pare nts m ust be fl ue nt i n 
E n glis h or S pa nis h. F or m ot hers w h o are marrie d or i n a marria g e- li ke relati o ns hi p, t heir 
part ners m ust als o c o nse nt t o partici pate. Partici p a nts will self -i de ntif y t heir preferre d 
la n g ua ge ( E n glis h or S pa nis h) 
 
Alt h o u g h t his st u d y will f oc us o n ne w b or ns, i n or der t o i ncrease o ur n u m b ers of 
pr os pecti ve s u bjects i n t h e “ Dia g n ose d C o h ort,” w e will e nr oll c hil dre n u p t o a ge 5 
years. I n or der t o o btai n m ore mea ni n gf ul dat a fr o m W E S a nal ysis, partic ul arl y f or 
c o n diti o ns s uc h as P K U, i ncl u di n g deter mi ni n g a n y ge n ot y pe- p he n ot y pe c orrelati o ns or 
i nfl ue nce of ot h er ge n etic fact ors, it is i m p orta nt t o o btai n cli nical data i n c hil dre n be y o n d 
i nfa nc y. T he “ Well- C hil d C o h ort” will c o nsist of ne w b or ns i n or der t o m ore acc uratel y 
reflect t he t y pical a ge of N B S.  
 
Pre g na nt w o me n a n d t heir part ners will be recr uite d fr o m t he Pre natal cli nics at U N C a n d 
verificati o n of t heir pre g na nt stat us will be b y self-i de ntificati o n a n d b y det er mi ni n g t hat 
t he y are b ei n g f oll o we d i n t he pre natal cli nics a n d ha ve ha d t heir pre g n a nci es verifie d as 
part of sta n dar d pre n atal care.  
 
A nti ci p at e d N u m b er of R e s e ar c h  S u bj e ct s  
Recr uit me nt will use esta blis he d c ha n nels at U N C, a n d we e x p ect t hat ~ 8 0 % of m ot hers 
we a p pr o ac h f or recr uit me nt will ha ve a part ner w h o is reas o na bl y a v aila ble a n d w h o 
t heref or e w o ul d be a p pr o ac he d f or recr uit me nt. 
 
F or t he “ Dia g n ose d C o h ort,” t here are 5 6 0 c urre nt pe diatric patie nts u n der a ge 5 wit h t he 
selecte d c o n diti o ns bei n g f oll o we d at U N C, a n d a n a d diti o nal 3 3 0 i nfa nts u n der 6 m o nt hs 
ol d are dia g n ose d eac h y ear. We esti mate t hat ~ 8 0 % of pare nts of c hil dre n i n t he 
“ Dia g n ose d” c o h ort will elect t o ha ve t heir c hil d u n der g o se q ue n ci n g. T h us, i n or der t o 
se q ue nce 2 0 0 c hil dre n i n t his c o h ort, we a ntici pate e nr olli n g 2 5 0 fa mil y u nits (c o u ples or 
si n gle pare nts, a n d t heir c hil d). 
 
F or t he “ Well - C hil d C o h ort,” t here are a p pr o xi matel y 3, 5 0 0 e x pecta nt m ot hers at U N C 
per year w h o will be eli gi ble, pr o vi di n g a lar ge p o p ulati o n fr o m w hic h t o recr uit. I n o ur 
pri or st u d y o n ne w b or n s cree ni n g f or fra gile X s y n dr o me ( F X S), 6 4 % of c o u ples a gree d 
t o j oi n t he st u d y a n d acce pte d scree ni n g. We t heref ore esti mate t hat ~ 6 4 % of pare nts 
a p pr oac h e d f or recr uit me nt t o t he “ Well - C hil d C o h ort” will a gree t o j oi n it, alt h o u g h t his 
esti mate is c o nser vati ve beca use j oi ni n g o ur st u d y will n ot necessitate als o acce pti n g 
N G S -N B S. We pr oject a 5 % dr o p o ut rate b et wee n Ti mes 1 – 3 ( w he n pare nts are acti vel y 
i n v ol ve d i n ma ki n g decisi o ns a n d recei vi n g res ults) a n d a n a d diti o nal 5 % dr o p o ut at 
Ti me 4. I n or der t o se q u e nce 2 0 0 c hil dre n i n t his c o h ort, we a ntici pate e nr olli n g 3 5 0 
eli gi ble fa mil y u nits. 

 
 
Base d o n t hese esti mates, we will a p pr oac h 4 8 pare nts per m o nt h o ver 2 0 t o 2 1 m o nt hs 
f or recr uit me nt t o yiel d a sa m ple of 4 0 0 c o m pleti n g t he st u d y o ver a p pr o xi matel y 3 0 
m o nt hs ( 2 0 0 eac h i n t he dia g n ose d c o h ort a n d well-c hil d c o h ort). 
 
I n cl u si o n Crit eri a  
 
“ Di a g n os e d C o h ort ” 
 
Pare nts meeti n g t he f oll o wi n g criteria:  
1.  Pare nts of a c hil d w h o meets t he criteria bel o w  A N D  
2.  At least 1 8 years  ol d. 
3.  F or m ot hers w h o are m arrie d or i n a marria ge- li ke relati o ns hi p, t heir part ners 
m ust als o c o nse nt t o partici pate. M ot hers w h o are n ot marrie d or n ot i n a 
marria ge -li ke relati o ns hi p will be a ble t o partici pate i n di vi d uall y. 
4.  M ust be a ble t o pr o vi de i nf or me d c o ns e nt f or t heir c hil d a n d f or t he msel ves 
5.  M ust be fl ue nt i n E n glis h or S pa nis h 
 
C hil dre n meeti n g t he f oll o wi n g criteria:  
1.  I nfa nts a n d c hil dr e n fr o m 0- 5 years  
2.  Dia g n ose d wit h k n o w n or s us pecte d m o n o ge nic dis or der, s uc h as:  
- P he n yl ket o n uria 
- Me di u m c hai n ac yl - C o A-de h y dr o ge n ase d eficie n c y  ( M C A D D) 
- C ystic fi br osis or C F T R -relate d meta b olic s y n dr o me. 
- C o n ge nital heari n g l oss 
- Ot her r are dis or d ers s uc h as pri mar y ciliar y d ys ki nesia or 
m uc o p ol ysacc hari d osis 
O R  
- T h ose wit h p ositi ve ne w b or n scree ns b ut n o n-c o nfir mat or y f oll o w- u p testi n g 
(“false p ositi ves”) 
3.  Me dicall y  sta ble 
 
“ W ell -C h il d C o h ort ”  
 
Pare nts meeti n g t he f oll o wi n g criteria:  
6.  Pre g na nt wit h a n i ntra uteri ne pre g n a nc y of 1 8 wee ks or greater  
7.  At least 1 8 years  ol d 
8.  F or m ot hers w h o ar e marrie d or i n a marria ge -li ke relati o ns hi p, t heir part ners m ust 
als o c o nse nt t o partici pat e. M ot hers w h o are n ot marrie d or n ot i n a marri a ge -li ke 
relati o ns hi p will be a ble t o partici pate i n di vi d uall y. 
9.  M ust be a ble t o pr o vi de i nf or me d c o ns e nt f or t heir c hil d a n d f or t he msel v es 
1 0.  M ust be fl ue nt i n E n glis h or S pa nis h 
1 1.  Ha ve n o pe n di n g or p ositi ve pre natal di a g n ostic test res ults f or  c o n g e nital 
malf or mati o ns or c hr o m os o mal a b n or malities  
1 2.  Ha ve bee n i de ntifie d b y me dical pers o n n el i n t he O B cli nic as p ossi ble ca n di dates.  
1 3.  C o u ples recr uite d i nt o t h e Well - C hil d c o h ort w h o deli ver at a n o utsi de l ocati o n ( n ot 

 
at U N C Hos pitals) will be all o we d t o partici p ate.  C o u ples w h o are n ot pati e nts of 
t he pre natal cli nic b ut w h o ha ve c o ns ulte d wit h t he m f or ser vices s uc h as 
ultras o u n ds a n d w h o c o ntact us as ki n g t o partici pate ma y c o me t o t he W o m e ns' 
H os pital a n d be recr uite d i nt o t he st u d y b y t he pre natal recr uiter.    
 
Ne w b or ns: 
1. Ha ve n o c o m plicati o ns at t he ti me of birt h or u n e x pecte d m e dical pr o ble ms; 
h o we ver, d e pe n di n g o n t heir cli nical c o urs e, t h ose w h ose pare nts ha ve pre vi o usl y 
c o nse nte d t o t he st u d y ma y ha ve D N A sa m pli n g o nce sta bilize d a n d dis c har ge d 
fr o m t he Ne o n atal I nte nsi ve Care U nit, if t he pare nts a gree. 
 
E x cl u si o n  Crit eri a  
 
Pare nts:  
1.  Y o u n ger t ha n 1 8 y ears ol d 
2.  U n willi n g t o c o m plete st u d y  pr oce d ures 
3.  Ha ve c o g niti ve or ot h er i m pair me nts t hat precl u de t he m gi vi n g i nf or me d c o nse nt  
4.  Disa gree a b o ut t heir c hil d’s partici pati o n  
5.  Tra nsfer t heir pr e natal care t o a n ot her  i nstit uti o n 
6.  Are n ot fl ue nt i n E n glis h or S pa nis h 
 
C hil dre n: 
1.  D o n ot meet dia g n ostic criteria as  a b o v e 
2.  Me dicall y  u nsta ble 
3.  Me dical care tr a nsferre d t o a n ot her  i nstit uti o n 
4.  N ot b or n at U N C H os pitals i n C ha pel Hill,  N C  
 
R e cr uit m e nt a n d e nr oll m e nt  pr o c e d ur e s  
After ha vi n g b ee n i de ntifie d b y t heir cli nicia n as eli gi ble, c o u ples will be c o ntacte d b y a 
st u d y recr uiter, a n d as ke d if t he y w o ul d li ke t o hear a b o ut t he st u d y. Fat hers will als o be 
recr uite d if t h e y ar e reas o na bl y a vaila ble. T h us, t h ese pr oce d ures dis c uss t he i n v ol ve me nt 
of “ par e nts.” H o w e ver, w he n fat hers are n ot reas o na bl y a vaila ble, m ot hers ma y 
partici pate o n t heir o w n. F or t h ose i n a c o u ple rel ati o ns hi p pare nts m ust be c o nc or da nt i n 
t heir decisi o ns t o c o nse nt or t he c o u ple will n ot be eli gi ble. 
 
T h e “ W ell -C hil d  C o h ort ”:  
 
I niti al C o nt act: T he r ecr uiter will a p pr oac h t h ose pre g na nt c o u ples i n t he U N C pre natal 
cli nic w h o ha ve b ee n i de ntifie d as p ote ntiall y eli gi ble a n d w h o ha ve b ee n 
i nf or me d a b o ut t he st u d y b y t heir cli nicia n. 
•  N ot eli gi ble: We will t ha n k t he m f or t heir ti me, n ot gat her a n y i nf or m ati o n, a n d 
n ot c o ntact t he m a gai n.  
•  Decli ners : We will t ha n k t he m f or t heir ti me, n ot gat her a n y i nf or mati o n, a n d n ot 
c o ntact  t he m a g ai n. 
•  Acce pt ers : T he recr uiter will briefl y descri be t h e st u d y a n d gi ve t he c o u ple a 

 
st u d y br oc h ure ( N E X U S Recr uit me nt Br oc h ure f or t he Well-c hil d c o h ort: 
A p pe n di x 1 0) t hat descri bes st u d y pr oce d ures, ge n o mic se q ue nci n g, t he ki n ds of 
c o n diti o ns t hat c o ul d be i de ntifie d, t he ra n d o mizati o n pr ocess, a n d a decisi o n 
ai dt o hel p t he m ma ke a d ecisi o n a b o ut j oi ni n g t he st u d y. T he y will als o be gi ve n 
a c o p y of t he c o nse nt f or m ( N E X U S Recr uit me nt Br oc h ure f or t he Well- c hil d 
c o h ort: A p pe n di x 1 0) a b o ut j oi ni n g t he st u d y t o rea d a n d t he i nta k e f or m f or eac h 
me m ber of t he c o u ple ( or j ust f or m ot hers if t he y are partici p ati n g wit h o ut a 
part ner). T he i nta ke f or m c ollects i nf or mati o n a b o ut de m o gra p hics, pre vi o us 
e x perie n ce wit h ge n etic testi n g, k n o wle d ge a b o ut ge n o mic se q ue nci n g, a n d 
pre g na nc y a n xiet y. C o u ples will be as ke d t o c o m plete t his f or m a n d bri n g it wit h 
t he m t o t he st u d y visit. 
 
T he c o u ple will be as k e d if t he y will a gree t o b ei n g c o ntacte d b y p h o n e b y t he st u d y 
sc he d uler t o as cert ai n t heir i nterest i n j oi ni n g t he st u d y. C o u ples w h o a gree will be as ke d 
f or t heir p h o ne n u m ber a n d c o ntact i nf or mati o n, i ncl u di n g e mail a d dress, a n d t heir 
la n g ua ge pr efere nce, w hi c h will be e ntere d i nt o t he st u d y data base ( R E D Ca p) al o n g wit h 
t he cli nic fr o m w hic h t he y were recr uite d a n d gest ati o nal a ge of t he pre g n a nc y. T he 
recr uiter will pr o vi de a ti mefra me f or t he call (e. g., a wee k) a n d as k t h at b ot h me m bers of 
t he c o u ple rea d t he st u d y br oc h ure a n d i nf or me d c o nse nt f or m bef ore t hat ti me a n d be 
prese nt o n t he call. 
 
F or t h ose w h o a gree t o j oi n, t he recr uiter will offer access t o t he first q uesti o n naire ( T 1 Q) 
i n eit her pa per f or m or electr o nic li n ks.  i P A D S will be a vaila ble f or us e b y t h ose w h o d o 
n ot ha ve a s mart p h o n e or ot her de vice.  If b ot h m e m bers of t he c o u ple are prese nt a n d 
ha ve ti me, t he y ca n als o access t he first decisi o n g ui de.  Alter nati vel y, if partici pa nts wis h 
t o wait u ntil t he y lea ve t he cli nic, or f or ti mes w h e n t he part ner is n ot prese nt, st u d y staff 
will e mail t he li n ks t o t he T 1 Q (see b el o w).   
 
Partici pa nts will  als o be se nt li n ks t o t he first electr o nic decisi o n g ui de; t hese li n ks bec o me 
acti ve aft er t he c o m pleti o n of t he T 1 Q.  F or c o u ples, eac h pare nt will c o m pl ete t he 
q uesti o n naire i n de pe n d e ntl y.  T he li n k will ta ke t he m t o a c o p y of t he i nf or mati o n pa ge 
t hat will i nstr uct t he m t hat b y pr ocee di n g t o t he q uesti o n naire, t he y will ha ve a gree d t o 
j oi n P hase I of t he st u d y.   
 
Recr uit m e nt p h o ne c all : T he st u d y sc he d uler will call t he c o u ple a n d as k if t he y w o ul d 
li ke t o j oi n t he st u d y. 
•  Decli ners : C o u ples w h o i n dicate t he y are n ot i ntereste d i n j oi ni n g t he st u d y will 
be as ke d t o pr o vi de b asic de m o gra p hic dat a a n d a reas o n f or decli ni n g. 
C o m pleti o n of t his ste p will e n d t heir partici pati o n a n d t heir i de ntif yi n g 
i nf or mati o n will be s hre d de d. 
•  Acce pt ers: We will o btai n t h e c o u ple’s ver b al c o nse nt f or P hase 1; j oi ni n g t he 
st u d y. 
 
If b ot h pare nts h a ve n ot r ea d t he st u d y br oc h ure a n d t he c o nse nt f or m b y t he ti me t he 
sc he d uler calls, t he y will be gi ve n a d diti o nal ti me t o rea d it, a greei n g o n h o w m uc h ti me 
t hat will be. 
 

 
Pare nt s w h o ha v e access t o a n I nter n et-e n a ble d c o m p uter will t he n be pr o vi de d wit h a 
li n k t o access t he Ti me 1 q uesti o n naire. Eac h m e m ber of t he c o u ple will c o m plete t he 
q uesti o n naires i n t he st u d y i n de pe n de ntl y. 
 
After c o m pleti n g t he Ti me 1 q uesti o n naire, t he y will be gi ve n access t o t he o nli ne 
electr o nic d ecisi o n ai d. T he decisi o n ai d will pr o vi de i nf or mati o n a b o ut se q ue nci n g a n d 
t he t y pes of res ults a vaila ble, t he fre q u e nc y of s u c h fi n di n gs, t he ris ks a n d be nefits of 
st u d y partici pati o n, a n d g ui de pare nts t hr u t he d ecisi o n- ma ki n g pr ocess. Pare nts will be 
e nc o ura g e d t o vie w t he d ecisi o n ai d bef ore t he st u d y visit a n d ca n use it t o i n dicate t heir 
c h oice of o n e of t hree o pti o ns: 
( 1) n ot i ntereste d a n d d o n ot wis h t o sc he d ule a visit, or 
( 2) i ntereste d a n d w a nt t o sc he d ule a st u d y visit, or 
( 3) u n deci de d a n d wa nt t o sc he d ule a st u d y visit t o lear n m ore.  
 
T h us, c o u ples ar e n ot e x pecte d t o ma ke a decisi o n at t his ti me a n d will ha ve a m ple ti me 
t o gat her i nf or mati o n a n d c o nsi der t heir o pti o ns. 
 
Pare nts w h o d o n ot ha ve i nter net acce ss will be m aile d a c o p y of t h e Ti me 1 
q uesti o n naire wit h i nstr ucti o ns t o ret ur n t he c o m plete d c o p y i n a pre- pai d e n vel o pe. 
T he y will t he n vie w t he decisi o n ai d at t he st u d y visit. 
 
T h ose w h o a gr ee t o a st u d y visit will be sc he d ule d a n d se nt i nf or mati o n a b o ut t he 
a p p oi nt me nt ti me, date a n d l ocati o n of t he visit. 
•  N o n -c o m pli a nt decli ners: C o u ples w h o ver ball y c o nse nt t o t he st u d y b ut w h o d o 
n ot s uccessf ull y sc he d ule a st u d y visit or w h o fail t o a p pear f or t heir sc h e d ule d 
st u d y visit will be as ke d if t he y w o ul d be willi n g t o resc he d ul e t heir visit. If n ot, 
t he y will be c o nsi dere d t o be decli ners. Decli ners will be as ke d t o pr o vi de basic 
de m o gra p hic i nf or m ati o n (f or c o m paris o n t o t he acce pters) a n d t heir reas o ns f or 
decli ni n g . C o m pleti o n of t his ste p will e n d t heir partici pati o n i n t he  st u d y. 
 
St u d y Visit Acti vities: C o u ples w h o sc he d ule a st u d y visit will meet i n pers o n wit h a 
ge netic c o u nsel or w h o will c ollect t heir c o m plete d i nta ke f or m, assess t heir healt h 
literac y a n d n u merac y wit h a vali date d brief i nter vie w, a n d disc uss a n y iss u es ge nerate d 
b y t he electr o nic d ecisi o n ai d a b o ut acce pti n g or decli ni n g se q ue nci n g of t heir c hil d. T he 
c o u nsel or will a ns wer q u esti o ns a n d assess t heir u n dersta n di n g of mai n p oi nts of 
i nf or me d c o nse nt i ncl u di n g t he ra n ge of res ults t hat c o ul d be ret ur ne d, t he pla n ne d use 
a n d st ora ge of ge netic d ata as well as t he ris ks a n d be nefits of ge n o mic s e q ue nci n g . 
C o nse nt (f or P h ase II; s e q ue nci n g) will be o bt ai ne d fr o m b ot h me m bers of t he c o u ple 
e xce pt i n cases w here t he fat her is n ot reas o na bl y a vaila ble. I n t h ose cases o nl y t he 
m ot her will be c o nse nte d. 
 
I n cases w he n o ne p are nt is u na ble t o atte n d t he st u d y visit, we will use S k y pe f or t he 
c o u nseli n g a n d c o nse nt pr ocess. T he S k y pe c o u ns eli n g a n d c o nse nt will be d o ne i n t he 
C T R C a n d will be c o n d ucte d b y t he cli nical ge n eticist a n d/ or ge netic c o u ns el or. T he 
part ner w h o is u n a ble t o atte n d will si g n t he c o nse nt f or m d uri n g t he e nc o u nter a n d 
ret ur n it t o t he st u d y office. 
 

 
•  Se q ue nci n g c o nse nters : After c o ns e nti n g, c o u ples will c o m plete t he Ti me 2 
q uesti o n naire a b o ut t heir decisi o n, m o o d, a n d k n o wle d ge a b o ut t he pr oj ect. T he y 
will als o be as ke d t o pr o vi de c o nse nt f or access t o t heir c hil d’s state ne w b or n 
scree ni n g r es ults a n d perti ne nt me dical rec or ds. 
•  Se q ue nci n g decli ners : Pare nts w h o decli ne se q ue nci n g will be as ke d t o c o m plete 
t he Ti me 2 q uesti o n naire a n d will e xit t he st u d y. 
•  C o u ples w h o are u ns ure a b o ut t heir se q ue nci n g decisi o n:  T he c o u ple ca n 
defer t h eir decisi o n a b o ut se q ue nci n g a n d d efer sc he d uli n g a st u d y visit. T his 
o pti o n will pr o vi de a d diti o nal ti me f or pare nts t o vie w t he decisi o n ai d a n d ma ke 
a decisi o n a b o ut ge n o mic se q ue nci n g pri or t o gi vi n g birt h ( w hic h n or mall y occ urs 
ar o u n d 4 0 wee ks gestati o n). I n or der t o facilitate t he ti me c o u ples ha ve t o rea d t he 
i nf or me d c o nse nt f or ms a n d vie w t he el ectr o nic d ecisi o n ai d, we are pr o vi di n g 
access t o t hese pri or t o a n d after t he st u d y visit.  T he y will ha ve a m ple ti me t o 
ha ve t heir q uesti o ns a ns were d, a n d c o nfer wit h ot hers bef ore pr o vi di n g c o nse nt 
(e. g., fa mil y me m bers, h ealt hcare pr o vi ders). 
•  If a n d w h e n a deferri n g c o u ple deci des t o pr o cee d, t he y will c o ntact t he st u d y 
office a n d a st u d y visit will be sc he d ule d (see a b o ve: st u d y acti vities). T he 
ge netic c o u nsel or will re vie w t he i nf or mati o n a n d o btai n c o nse nt. After 
pr o vi di n g c o nse nt f or se q ue n ci n g, c o u ples will c o m plete t he Ti me 2 
q uesti o n naire as des cri be d a b o ve. T he y will als o be as ke d t o pr o vi de c o nse nt f or 
access t o t heir c hil d’s state ne w b or n scree ni n g res ults a n d perti ne nt me dical 
rec or ds. 
 
C o u ples ca n c ha n g e t heir decisi o n fr o m yes t o n o bef ore t h e sa m ple is o btai ne d after t h e 
ba b y is b or n. T he y will be as ke d a b o ut t heir decisi o n, c o m plete t he Ti me 2 q uesti o n naire 
a gai n a n d e xit fr o m t he st u d y. 
 
T h e “ Di a g n o s e d  C o h ort ”: 
Ma n y of t hese f a milies li ve l o n g dista nces fr o m U N C a n d we w o ul d li ke t o c o or di nate 
t he st u d y visit wit h a n u pc o mi n g cli nical visit w hic h necessitates t hat we c o ntact t he m 
bef ore t h eir c hil d’s a p p oi nt me nt. All pare nts will ha ve first bee n i ntr o d uce d t o t he st u d y 
b y t heir c hil d’s cli nicia n eit her i n pers o n, b y p h o n e or b y a letter acc o m pa n yi n g t he st u d y 
pa m p hlet. 
 
I niti al C o nt act: Pare nts will be c o ntacte d b y mail bef ore t h eir u pc o mi n g cli nic visit a n d 
se nt t he st u d y br oc h ure a n d a letter fr o m t heir c hil d’s cli nicia n i n viti n g t he m t o 
partici pate wit h a n o pt- o ut p ostcar d t o ret ur n if t h e y wis h t o decli ne. T he y will als o be 
se nt a c o p y of t he c o nse nt f or m t o j oi n t he st u d y. If pare nts d o n ot o pt o ut, t he y will be 
c o ntacte d 2 -4 wee ks l ater b y a tele p h o ne call or recr uite d at t he ti me of t heir c hil d’s 
a p p oi nt me nt. 
 
P h o ne c all recr u it m e nt a n d st u d y visit sc he d uli n g: as descri be d a b o v e 
 
I n-Pers o n Recr uit m e nt: S o me pare nts ma y n ot b e reac ha ble b y p h o n e bef ore t heir 
c hil d’s cli nic visit. I n t hese cases, a st u d y recr uiter will as k t he m if t he y wa nt t o j oi n t he 
st u d y at t he ti me of t heir c hil d’s cli nic visit. W he n p ossi ble, t he y will ha ve alrea d y b ee n 
se nt t he recr uit me nt br oc h ure a n d t he c o nse nt f or m t o j oi n t he st u d y. If t he y wis h t o j oi n, 

 
t he y ca n gi ve v er bal c o ns e nt f or P hase I (j oi ni n g t he st u d y) a n d c o m plete t he i nta ke f or m. 
T he y will t he n c o m plete t he Ti me 1 q uesti o n naire ( o nli ne) a n d t he rest of t h e st u d y visit 
acti vities as descri b e d a b o ve. After t h e y c o m plete t he Ti me 1 q uesti o n naire, t he y will be 
pr o vi de d wit h a li n k t o t he electr o ni c decisi o n ai d. 
 
Pare nts w h o atte n d a st u d y vis it (i ncl u di n g t h ose w h o are recr uite d i n p ers o n) will meet 
wit h a ge netic c o u ns el or t o disc uss a n y q uesti o ns t he y ha ve a b o ut N G S- N B S a n d a b o ut 
acce pti n g or decli ni n g se q ue nci n g of t heir c hil d as descri be d f or t he “ Well- C hil d” c o h ort 
a b o ve. C o nse nt f or P has e II (c o ns e nt f or se q u e nci n g) will be o btai ne d fr o m t h ose w h o 
a gree.  
 
Decli ners: As d escri b e d a b o ve.  
Se q ue nce c o nse nters :  As descri be d a b o ve. 
Se q ue nce decli ners :  As descri be d a b o ve. 
 
St u d y tr e at m e nt a n d/ or di a g n o sti c  pr o c e d ur e s  
 
  
S a m ple C ollecti o n a n d D N A is ol ati o n: 
Sali va sa m ples will be c ollecte d b y trai ne d st u d y p ers o n nel usi n g Ora g e ne s p o n ge 
c ollecti o n kits. S p o n ges will be s wa b be d i nsi de t h e c hee ks a n d al o n g t he g u ms of t he 
i nfa nt ( A p pe n di x 1). 
Nee d t o descri be t he pr o ce d ures of c ollecti o n of sali va (a n y k n o w n i nfere nces s uc h f or 
f orei g n s u bsta nces) a n d trac ki n g/li n ki n g sa m ples wit h partici pate. 
 
•  I n t he “ Well- C hil d C o h ort,” arra n ge me nts will be ma de t o c o ntact us w h e n t he 
ba b y is b or n t o o btai n t he sa m ple. T he PIs will be n otifie d t hr o u g h E PI C at t he 
ti me of t he i nfa nt’s deli v er y. T he b u ccal s w a b will be o btai ne d d uri n g t he ba b y’s 
sta y at U N C H os pitals f oll o wi n g his or her deli ver y or at a f ut ure well-b a b y 
a p p oi nt me nt at a U N C cli nic or at a p ost part u m cli nic visit f or t he  m ot her. 
 
•  I n t he “ Dia g n os e d C o h ort,” t he b uccal s wa b will be o btai ne d aft er pare ntal 
c o nse nt t o se q ue nci n g is o btai ne d w hic h c o ul d occ ur at t he ti me of st u d y visit or 
at a f ut ure i n -p ers o n  visit).  
 
D N A will be is olate d fr o m d u plicate sa m ples usi n g sta n dar d pr o ce d ures i n t he U N C B S P 
a n d t he C LI A- certifie d M olec ular Dia g n ostic L a b orat or y ( M S MI D N A e xtracti o n fr o m 
O C - 1 7 5 c ollecti o n s yste ms: see A p pe n di x 2 a n d M ol Ge n Ne w b or n Sali v a E xtracti o n b y 
Bi o R o b ot E Z 1: see A p pe n di x 3). 
 
E x o m e  S e q u e n ci n g:  
A n ali q u ot fr o m eac h u ni q uel y c o de d D N A sa m pl e will be tra nsferre d b y t he B S P t o t he 
la b of Dr. J o nat h a n Ber g, M D, P h D, Ass ociate Pr ofess or i n t he De p art me nt of Ge netics at 
U N C. Sa m ples will be s u bjecte d t o N G S usi n g w h ole e x o me se q ue n ci n g ( W E S) as 
descri be d i n secti o n 2. ( A gile nt S S E L A ut o mate d Tar get E nri c h me nts: see A p pe n di x 5).  
Se q ue nci n g li braries will be tra nsferre d t o t he H T S F f or massi vel y parallel se q ue nci n g 
usi n g t he Ill u mi na Hi Se q 2 0 0 0 or Hi Se q 2 5 0 0 platf or m ( A p pe n di x 6). 

 
C ha n ges i n tec h n ol o g y ma y alter t he c h oice of t ar g et ca pt ure or se q u e n ci n g platf or m, 
w hic h mi g ht affect t he yiel d of p ositi ve res ults b ut w o ul d n ot affect t he nat ure of res ults 
ret ur ne d. 
 
Bi oi nf or m ati c s:  
Ra w se q ue nce data fr o m t he H T S F will be a nal y ze d usi n g sta n dar d bi oi nf or matics 
met h o ds t o ma p se q ue nce fra g m e nts a n d ali g n t he m t o t he refere nce h u ma n 
ge n o me. Ge n etic varia nts will be i de ntifie d usi n g a c ust o m pi peli ne t hat has bee n 
de vel o pe d i n c olla b or ati o n wit h c ollea g ues i n t he De part me nt of Ge netics a n d t he 
Re naissa nce C o m p uti n g I nstit ute ( R E N CI). T h e c urre nt pi peli ne is as f oll o ws: 
 
• 
Fra g me nts are ali g ne d a g ai nst a n i n de xe d refere nce h u ma n ge n o me ( N C BI 3 7. 1 / 
h g 1 9) usi n g B W A  
• 
Res ulti n g S A M files are s orte d, i n de xe d, a n d c o n verte d t o bi nar y B A M fil es usi n g 
Picar d a n d  S A Mt o ols. 
• 
P ost-ali g n me nt o pti mizati o n, i ncl u di n g P C R d u plicate re m o val, reali g n me nt of 
rea ds, a n d q u alit y sc ore recali brati o n are perf or m e d usi n g T he Ge n o me A nal ysis 
T o ol kit ( G A T K). 
• 
Si n gle n ucle oti de varia nts a n d s mall i nserti o ns a n d deleti o ns are calle d usi n g t he 
G A T K U nifie d  G e n ot y per. 
• 
Q ualit y metrics will b e i nc or p orat e d s o t hat c o vera ge wit h q ualit y sc ores ca n be 
assesse d f or a n y gi ve n n u cle oti de.  
 
Ge netic varia nts i de ntifie d (a p pr o xi matel y 1 0 0, 0 0 0 per i n di vi d ual e x o me) will be 
de p osite d i n a de dicat e d data base a n d will be e xte nsi vel y a n n otate d a n d s u bjecte d t o i n 
silic o a nal ysis. A n n otati o ns t hat will be a p plie d t o t he varia nts a n d re vie w e d b y t he 
a nal ysts w h o i nter pret t h e varia nts are as f oll o ws: 
• 
Ref Se q tra nscri pts, wit h pr otei n effects  
• 
1 0 0 0 ge n o mes pr oject a n d E x o me A g gre g ati o n C o ns orti u m ( E x A C) varia nt 
fre q ue n c y data  
• 
H u ma n Ge ne M ut ati o n Data base ( H G M D) m utati o ns a n d Cli n Var pat h o ge nicit y 
asserti o ns  
• 
A d diti o nal a n n otati o ns are p ossi ble, s uc h as d b S N P e ntr y, O MI M i de ntifiers, 
e v ol uti o nar y c o nser v ati o n, P ol y p he n a n d ot her pr otei n pre dicti o n al g orit h ms.  
• 
C urate d refer e nces fr o m t he bi o me dical  literat ure. 
 
C at e g ori z ati o n of p o s si bl e g e n o mi c  i nf or m ati o n: 
I n or der t o e v al uate t he r a n ge of ge n o mic fi n di n gs, we utilize a fra me w or k f or “ bi n ni n g” 
ge nes i nt o cate g orical lists t hat will facilitate i nf or me d decisi o n -ma ki n g. We will utilize 
t he f oll o wi n g cate g ori es of ge n o mic res ults i n t his st u d y: 
 
1.  Ne xt -Ge ner ati o n Se q ue nci n g Ne w b or n Scree n ( N G S -N B S): Me dicall y 
acti o na ble c hil d h o o d c o n diti o ns, re prese nti n g t he c ore res ults t hat will be ret ur ne d 
t o all partici pa nts i n t he st u d y. T he N G S- N B S i ncl u des ge nes i m plicate d i n 
c o n diti o ns t hat are c urre ntl y scree ne d f or i n sta n dar d state ne w b or n scree ns, 

 
i ncl u di n g meta b olic dis or ders, e n d ocri ne dis or ders, a n d heari n g l oss. I n a d diti o n, 
we will i ncl u de ot her me dicall y acti o na ble c o n diti o ns t hat are n ot a me n a ble t o 
c urre nt scree ni n g met h o ds b ut ca n be detecte d usi n g ge netic se q ue n ci n g (e. g. 
here ditar y ca n cer s usce pti bilit y wit h o nset or i nitiati o n of scree ni n g pr ot o c ols i n 
c hil d h o o d). T he criteria f or deter mi ni n g w hic h ge nes t o i ncl u de i n t he N G S- N B S 
are part of t he o verall ai ms of t he researc h pr oject (see bel o w). T hese fi n di n gs 
re pres e nt t he def a ult set of res ults t hat w o ul d be ret ur ne d wit h e ver y se q ue nci n g 
re p ort. All par e nts c o nse nti n g t o se q ue nci n g of t heir c hil d will lear n if t heir c hil d 
has o ne or m or e varia nts i n t his cate g or y t hat are d eter mi ne d t o i n dicate wit h hi g h 
li keli h o o d t hat t he c hil d has or will li kel y de vel o p a partic ular ge netic dis or der. 
 
 
2.  A d diti o n al ge n o mic fi n di n gs: C o n diti o ns t hat d o n ot meet t he t hres h ol d f or 
i ncl usi o n i n t he N G S- N B S. O nl y pare nts ra n d o mize d t o t he “ decisi o n” gr o u p will 
be as ke d t o deci de if t he y wis h t o lear n a n y, all or n o ne of t hese a d diti o nal 
fi n di n gs. H u ma n c urati o n a n d a nal ysis of t hese v aria nts will n ot be perf or me d 
u ntil pare nts re q uest t he m. T his a nal ysis w o ul d n ot be d o ne f or c hil dre n i n t he 
c o ntr ol gr o u p (see ra n d o mizati o n pr oce d ure bel o w).  T hese a d diti o nal fi n di n gs 
fall i nt o t he f oll o wi n g cate g ories:  
 
A.  
Me dic ally - a cti o n a ble a d ult o nset c o n diti o ns: T hese dis or ders w o ul d be 
si milar t o t he ki n ds of res ults descri be d i n N G S- N B S (a b o ve) b ut are relat e d t o 
c o n diti o ns i n w hic h t he o nset or i nitiati o n of scree ni n g pr ot oc ols occ urs i n 
a d ult h o o d, s uc h as Here ditar y Breast a n d O v aria n Ca ncer g e ne m utati o ns.  
 
B.  
N o n- me dic ally acti o n a bl e c hil d h o o d o nset c o n diti o ns : T he fi n di n gs i n t his 
gr o u p relate t o c hil d h o o d healt h c o n diti o ns t hat ha ve n o s pecific m e dical 
i nter ve nti o ns. T his cate g or y i ncl u des ge nes i m plicate d i n ge n etic dis or ders f or 
w hic h n o s pecific pre ve nti ve meas ure or treat me nt has bee n s h o w n t o m iti gate 
m or bi dit y. E xa m ples i ncl u de Rett s y n dr o me a n d A n gel ma n s y n dr o me, c o n diti o ns 
ass ociate d wit h i ntellect u al disa bilit y i n c hil d h o o d f or w hic h t here is n o me dical 
treat me nt, b ut f or w hic h earl y i de ntificati o n a n d i nitiati o n of t hera p y ser vi ces are 
be ne ficial. 
 
C.  
C arrier st at us : T his cate g or y relates t o fi n di n gs t hat ha ve re pr o d ucti ve 
i m plicati o ns, s uc h as carrier stat us f or recessi ve dis or ders s uc h as c ystic fi br osis 
a n d Fa n c o ni a ne mia.  
 
3.  E xcl u de d ge n o mic fi n di n gs ( N o n- me dic ally acti o n a ble a d ult o nset c o n diti o ns): 
I n k ee pi n g wit h et hical n or ms i n t he fiel d a n d t o pr otect a c hil d’s ulti mate 
a ut o n o m y, we ha ve d efi n e d a pr ocess f or c h o osi n g ge nes t hat w o ul d be e xcl u de d 
fr o m a nal ysis a n d w o ul d n ot be ret ur ne d, re gar dless of t he ra n d o mizati o n st at us. 
T h us, n o p a rtici p a nts will recei ve g e n o mic res ults rel ate d t o n o n -me dic all y 
acti o n a ble a d ult o nset c o n diti o ns . T his cate g or y is e xe m plifie d b y c o n diti o ns 
s uc h as a m y otr o p hic lateral scler osis ( A L S). 
 

 
D efi ni n g Cli ni c al  A cti o n a bilit y:  
We ha v e de vel o p e d a se mi - q ua ntitati ve metric f or sc ori n g t he acti o na bilit y of ge ne- 
disease pairs i n or d er t o f acilitate t heir assi g n me nt i nt o “ bi ns” use d t o g ui de t he ret ur n of 
res ults ( 3 0). T his fr a me w or k has bee n a d o pte d b y t he N C N E X U S pr oject, a n d we ha v e 
asse m ble d a di vers e gr o u p of e x perts a n d sta ke h ol ders t o s yste maticall y ass ess ge nes 
i m plicate d i n Me n delia n disease. T his met h o d ass esses eac h ge ne- diseas e pair t hr o u g h 
t he f oll o wi n g fi ve q uesti o ns: 
 
1)  W hat is t he nat ure of t he t hreat t o healt h f or a n i n di vi d ual carr yi n g a p at h o g e nic 
allele of t he gi ve n g e ne? ( Ra n gi n g fr o m s u d de n deat h t o n o p he n ot y pic i m pact) 
2)  W hat is t he c ha n ce t hat t his t hreat will materialize? ( Relate d t o  pe n etra n ce)  
3)  H o w eff ecti ve are i nter ve nti o ns f or pre ve nti n g har m? ( A critical c o m p o ne nt of 
me dical  acti o na bilit y) 
4)  H o w acce pta ble are t h e i nter ve nti o ns i n ter ms of t he b ur de ns or ris ks place d o n t he 
i n di vi d ual? ( Reflecti n g t he p ossi ble hazar ds a n d d o w nsi des of me dical i nter ve nti o n) 
5)  W hat is t he k n o wle d ge- b ase re g ar di n g t he nat ure of t he dis or der a n d its 
ma na ge me nt i n pre- s y m pt o matic i n di vi d uals? 
 
Eac h ge n e -diseas e pair recei ves a s c ore fr o m 0 t o 1 5, a n d we will deter mi n e a t hres h ol d 
le vel t hat i n dicates a le v el of me dical acti o na bilit y t hat j ustifies i ncl usi o n i n t he N G S- 
N B S.  
 
I n a d diti o n t o t he acti o na bilit y sc ore, eac h c o n diti o n will be c haracterize d i n ter ms of t he 
t y pical a ge of o ns et a n d a ge at w hic h i nter v e nti o ns w o ul d be i nitiate d. T h us, we ca n 
ge nerat e a t w o - di me nsi o nal re prese ntati o n of t he a ge- bas e d acti o na bilit y t hat ca n be us e d 
t o defi ne t he f o ur cate g ories descri be d a b o ve.  
•  C o n diti o ns t hat ha ve a n acti o na bilit y sc ore t hat e x cee ds t he t hres h ol d a n d h a ve 
o nset of disease or i nter v e nti o ns bef ore a ge 1 8 w o ul d be c o nsi dere d ca n di d ates f or 
N G S -N B S.  
•  C o n diti o ns t hat ha ve a n acti o na bilit y sc ore t hat e x cee ds t he t hres h ol d b ut ha ve 
o nset of disease or i nter v e nti o ns after a g e 1 8 w o ul d be i ncl u de d i n t he a d ult- o nset 
me dicall y acti o na ble cate g or y.  Ma n y ge netic c o n diti o ns ma y ha ve varia bl e a ges 
of s y m pt o m o nset i n eit her c hil d h o o d or a d ult h o o d, s uc h as P o m pe disease, 
Kra b be disease, Fa br y disease, or car di ac arr h yt h mias. F or t his reas o n, c o n diti o ns 
s uc h as t hese will be place d wit h c hil d h o o d- o nset c o n diti o ns. 
•  C o n diti o ns t hat ha ve a n acti o na bilit y sc ore bel o w t he t hres h ol d b ut ha ve o ns et 
bef ore a ge 1 8 w o ul d b e i ncl u de d i n t he c hil d h o o d- o nset n o n- me dicall y  acti o na ble 
cate g or y.  
•  C o n diti o ns t hat ha ve a n acti o na bilit y sc ore bel o w t he t hres h ol d a n d o nset after a ge 
1 8 w o ul d be i ncl u de d i n t he a d ult- o nset n o n- me dicall y acti o na ble cate g or y (a n d 
t h us n ot eli gi ble f or ret ur n of res ults). 
 
A list of c o n diti o ns t hat ha ve bee n sc ore d b y t he N C N E X U S tea m as of t he date of 
s u b missi o n are pr o vi de d i n N C N E X U S _ Acti o na bilit y Sc ores (see A p pe n di x 8). T he 
ta bles i n A p pe n di x 8 d oc u me nt t he i nitial w or k perf or me d i n t he N C N E X U S pr oject a n d 
pre vi o us w or k ( Ber g et al. 2 0 1 5) t o de vel o p a se mi- q ua ntitati ve metric f or assessi n g 
cli nical acti o na bilit y of g e ne - disease pairs. T his list of 6 5 8 ge ne- disease pairs is a w or k i n 

 
pr o gress a n d w e e x p ect t o c urate > 2 0 0 ge ne- disease pairs b y t he e n d of t h e N C N E X U S 
pr oject. Sc ores, ma y b e u p date peri o dicall y t o refl ect pr o gress i n t he e vi de n ce base or 
a d va nces i n ma na ge me nt of differe nt ge netic dis or ders. T hese s c ores will be use d, i n 
c o m bi nati o n wit h c urate d i nf or mati o n re gar di n g t he a ge of o ns et or a g e at w hic h 
i nter ve nti o ns w o ul d occ ur, t o defi ne t he f o ur cate g ories of ge n o mic i nf or m ati o n defi ne d 
i n t his pr ot oc ol. Si nce t he de vel o p me nt of fi nal lists c o n diti o ns i n eac h of t hese cat e g ories 
is a pri mar y o utc o me of t he st u d y, we a ntici pate t h at t he w or k of bi n ni n g eac h Me n delia n 
dis or der is e x pecte d t o c o nti n ue t hr o u g h o ut t he st u d y peri o d, a n d t hat peri o dic u p dates of 
t he lists will occ ur. T he F D A will be pr o vi de d wit h a 5- da y n otice of a n y u p dates or 
c ha n ges i n t he lists t hat are i m ple me nte d i n t he i nf or matics al g orit h ms. 
 
G e n eti c V ari a nt I nt er pr et ati o n a n d  R e p orti n g:  
A me m ber of t he st u d y tea m, acti n g as a m olec ular a nal yst, will c o n d uct a n i nitial re vie w 
of t he varia nt d ata, i ncl u di n g re vie w of q u alit y metrics, vis ual i ns pecti o n of varia nts, a n d 
re vie w of t h e literature. T he res ults of t he a n al ysis will be prese nte d t o t he m olec ular 
si g n-o ut c o m mittee ( b oar d -certifie d cli nical ge n eticists, ge netic c o u nsel ors, cli nical 
m olec ular ge n eticists a n d pat h ol o gists) f or disc ussi o n. Fi nal i nter pret ati o ns will be a d de d 
as part of t hat varia nt’s a n n otati o n i n t he data base, s o t hat f ut ure i nsta nces of t hat varia nt 
ca n be c o nsiste ntl y assi g ne d. T he researc h tea m will re vie w all vari a nts i de ntifie d as 
bei n g p ossi bl y re p orta ble (see bel o w f or det aile d pr oce d ures). T h ose j u d g e d t o be 
cli nicall y rele va nt w o ul d be c o nfir me d i n t he C LI A-certifie d M G L usi n g t he d u plicate 
D N A sa m ple.  
 
I n dicati o n-base d a nal ysis  
I n t he “ Dia g n os e d C o h ort,” we will perf or m a n “i n dicati o n-base d a nal ysis” t hat  e val uates 
varia nts i n ge nes wit hi n a s pecific dia g n ost ic list t hat is c o nstr ucte d s o as t o i nterr o gate 
all k n o w n ge nes t hat c o ul d be relate d t o a patie nt’s p he n ot y pe. I n t he setti n g of a 
dia g n ostic e val uati o n, we will re vie w all vari a nts i n ge nes t hat c o ul d be relate d t o t he 
p he n ot y pe, usi n g a c o m p utati o nal c lassifier t o pri oritize varia nts f or a nal ysis ( Ta ble 1).  
Si nce t hese i n di vi d uals are alr ea d y dia g n ose d wit h a rare ge n etic dis or der, we will ret ur n 
varia nts t hat ar e dee m e d t o be “ pat h o ge nic, ” “li kel y pat h o ge nic,” or “ varia nt of u ncertai n 
si g nifica nce, ” acc or di n g t o acce pt e d practice g ui d eli nes de vel o pe d b y t he A C M G. It 
s h o ul d be n ote d t hat t he c o m p utati o nal pri oritizati o n is strictl y i nte n de d as a wa y t o 
facilitate h u ma n r e vie w of t he data, a n d will n ot c o nstit ute a n a ut o mate d ass ess me nt of 
varia nt pat h o ge nicit y. F or i nsta nce, it has bee n o ur e x perie n ce i n pri or e x o me-se q ue n ci n g 
relate d st u dies t hat ma n y varia nts t hat ha d pre vi o usl y bee n i de ntifie d as pat h o ge nic i n 
data bases of h u ma n m utati o n ha ve s u bse q ue nt e vi de nce calli n g t his pat h o ge nicit y i nt o 
q uesti o n, s u p p orti n g t he nee d f or m a n ual re vi e w of varia nts e v e n i n t his hi g h- pri orit y 
class. 
 
Ta ble 1: C o m p utati o nal classificati o n of ge n o mic varia nts t o pri oritize f or h u ma n re vie w  
Class  Prese nt i n data base of 
h u ma n m utati o ns 1  
Varia nt T y pe 2  
Mi n or Allele 
Fre q u e n c y ( M A F) 6  
A  
Yes  
A n y  
< 5 %  
B  
N/ A  
Tr u ncati n g 3  
< 1 %  
C  
N/ A  
Misse nse  
< 1 %  

 
D  
N/ A  
S y n o n y m o us, N o n -ca n o nical 
s plice site4, a n d U T R5  
< 1 %  
E  
N/ A  
I ntr o ni c 
< 1 %  
F  
N/ A  
Tr u ncati n g a n d Misse nse  
1 -5 %  
 
G  
N/ A  
All ot her varia nts  
1 -5 %  
H  
N/ A  
A n y  
> 5 %  
1.  Data bases t o be use d i n t his c o m p utati o nal a nal ysis i ncl u de H G M D a n d t he N C BI Cli n Var data base. 
Varia nts t hat q ualif y f or cate g or y A are t h ose i de ntifie d as “ Disease M utati o n” ( D M) i n t he H G M D or 
varia nts i de ntifie d as “ Pat h o ge nic” or “ Li kel y Pat h o ge nic” i n  Cli n Var.  
2.  F or t he p ur p o se of c o m p utati o nal classificati o n, t he “ varia nt t y pe” will defa ult t o t he m ost da ma gi n g 
effect f or t he varia nt a m o n g all of t he tra nscri pts re prese nte d i n t he Ref Se q data base. F or e xa m ple, if t he 
varia nt has a misse nse effect i n o ne tra nscri pt b ut is i ntr o nic or U T R i n a n ot her tra nscri pt, it will be treate d 
as misse nse f or t he p ur p oses of c o m p utati o nal  classificati o n.  
3.  Tr u ncati n g  varia nts  i ncl u de: n o nse nse,  fra mes hifti n g i nserti o ns/ deleti o ns, a n d  ca n o nical s plice site 
alterati o ns (t he first t w o a n d last t w o  n ucle oti des of t he  i ntr o n). 
4.  N o n -ca n o nical s plice site vari a nts  i ncl u de t h ose t hat occ ur  wit hi n  3-1 0  n ucle oti des  of  t he i ntr o n-e x o n 
b or der.  
5.  U T R  varia nts  are a n n otate d  as bei n g  l ocate d i n t he 5’  u ntra nslate d  or  3’  u ntra nslate d  re gi o ns of  t he 
m R N A.  
6.  M A F  data will  be  deri ve d  fr o m fre q ue nc y data fr o m  t he 1 0 0 0  Ge n o mes  Pr oject  a n d  E x A C;  t he hi g hest  of 
t he mi n or allele fre q ue ncies f or a gi ve n varia nt fr o m a n y et h nic gr o u p will be use d t o e val uate t he M A F 
t hres h ol d criteria. 
 
I nte gral t o t he efficie nt di a g n ostic assess me nt of a n e ntire ge n o me or e x o m e will be t he 
esta blis h me nt of a pri ori pa nels of ge n es t o be ass esse d u n der cert ai n cli nical 
sit uati o ns. O ne of t he maj or tas ks of t he cli nical a n d m olec ular tea ms will be t he 
de vel o p me nt of s uc h lists rele va nt t o t he cate g ories of dis or ders t hat are prese nt i n t he 
Dia g n ose d C o h ort. O nce esta blis he d, t hese lists will be use d t o q uer y patie nts’ varia nt 
data t o i de ntif y all varia nts i n ge nes of p ossi ble dia g n ostic si g nifica nce i n t he c o nte xt of 
t heir me dical pres e ntati o n.  A m olec ular a n al yst will e val uate t he pri oritize d varia nt list 
a n d pr o vi de a preli mi nar y i nter pretati o n of t he cas e t o t he m olec ular si g n- o ut c o m mittee.  
 
T he c o m mittee will ma ke a fi nal pat h o g e nicit y deter mi nati o n a n d deci de w het her a n y 
varia nts e xcee d o ur t hres h ol d f or re p orti n g ( T a ble 2). Beca use of t he prese n ce of a 
p he n ot y pe i n t he i n di vi d ual bei n g se q ue nce d, res ults c o nsi dere d t o be cli nicall y rele va nt 
w o ul d i ncl u de t he “ k n o w n pat h o ge nic,” “li kel y pat h o ge nic,” a n d “ varia nt of u ncert ai n 
si g nifica nce” as deter mi ne d b y t he m olec ular si g n-o ut c o m mittee.  
 
Ta ble 2: Cate g ories of fi n di n gs dee me d re p orta bl e f or a n i n dicati o n- base d a nal ysis  
Res ult Cate g or y  
Varia nt t y pes  Z y g osit y  
P he n ot y pe 8  
I n h erita nce 
P ositi ve -Defi niti ve  K P 1  
Heter oz y g o us  
C o nc or da nt  
D o mi na nt 9  
K P  
H o m oz y g o us or 
c o m p o u n d 
heter oz y g o us 6  
C o nc or da nt  
Recessi ve 1 0  
P ositi ve -Pr o ba ble  
L P 2  
Heter oz y g o us  
C o nc or da nt  
D o mi na nt  
K P  
P ote ntiall y 
c o m p o u n d 
heter oz y g o us 7  
C o nc or da nt  
Recessi ve  

 
L P  
H o m oz y g o us or 
p ote ntiall y 
c o m p o u n d 
heter oz y g o us  
C o nc or da nt  
Recessi ve  
 
U ncertai n -V U S  
V U S 3  
Heter oz y g o us  
C o nc or da nt  
D o mi na nt  
V U S,  
H o m oz y g o us  
C o nc or da nt  
Recessi ve  
V U S pl us 
K P/ L P 4  
C o m p o u n d 
heter oz y g o us or 
p ote ntiall y 
c o m p o u n d 
heter oz y g o us  
 
 
U ncertai n -A R het  
K P/ L P 5  
Heter oz y g o us  
C o nc or da nt  
Recessi ve  
U ncertai n - 
C o ntri b ut or y  
A n y  
A n y  
Partiall y 
matc hi n g  
A n y  
1.  K P = K n o w n  Pat h o ge nic  
2.  L P = Li kel y  Pat h o ge nic  
3.  V U S = Varia nt of U ncertai n Cli nical  Si g nifica nce  
4.  I n c o n diti o ns wit h recessi ve i n herita nce, we ma y i de ntif y o ne K P or L P varia nt a n d o ne V U S. I n t his 
sit uati o n, we w o ul d re p ort t he fi n di n gs as a t y pe of “ U ncertai n” res ult d ue t o t he prese nce of o ne V U S 
allele. Pare ntal st u dies w o ul d be re q ueste d t o deter mi ne t he p hase of t he  varia nts.  
5.  I n c o n diti o ns wit h recessi ve i n herita nce i n w hic h we o nl y fi n d a si n gle K P or L P varia nt, b ut are u nable 
t o i de ntif y a sec o n d ca n di date varia nt,  we  will  re p ort t his fi n di n g as a t y pe of  “ U ncertai n”  res ult d ue  t o t he 
p ossi bilit y of a misse d e x o nic or partial ge ne deleti o n o n t he o p p osite  allele. 
6.  Wit h N G S tec h n ol o g y, it ma y n ot be p ossi ble t o deter mi ne t he p hase of t w o varia nts t hat are i de ntifie d. 
W he n p ossi ble, we will use data fr o m t he ali g ne d se q ue nce rea ds t o deter mi ne p hase.  If t he t w o varia nts 
ca n be s h o w n t o be o n o p p osite stra n ds usi n g N G S data, t he y will be re p orte d as “ P ositi ve -Defi niti ve” wit h 
p are ntal st u dies re q ueste d f or c o nfir mati o n of  p hase.  
7.  W he n ali g ne d se q ue nce data are u na ble t o deter mi ne t he p hase of t w o ca n di date varia nts, t he y will be 
dee me d “ p ote ntiall y c o m p o u n d heter oz y g o us” a n d re p orte d as a “ P ositi ve -Pr o ba ble” res ult u ntil pare ntal  
st u dies ca n be perf or me d t o deter mi ne p hase.  
8.  If t he p he n ot y pe  of  t he dia g n ose d  i n di vi d ual matc hes  wit h  t he c o n diti o n  pre dicte d  b y  t he ge netic  res ults, 
t his will be c o nsi dere d a “c o nc or da nt” res ult. H o we ver, if t he p he n ot y pe of t he dia g n ose d i n di vi d ual o nly 
partl y matc hes or is i nc o m pletel y e x plai ne d b y t he ge netic res ults, t his will be c o nsi dere d a “ partiall y 
matc hi n g” res ult. I n cases wit h “ partiall y matc hi n g” p he n ot y pe, t he res ult will defa ult t o a n “ U ncertai n - 
C o ntri b ut or y” res ult c o m m u nicate d wit h a p pr o priate  ca veats. 
9.  D o mi na nt i n herita nce i ncl u des b ot h a ut os o mal a n d X -li n ke d d o mi na nt c o n diti o ns. F or X-li n ke d 
d o mi na nt  c o n diti o ns rele va nt varia nts  w o ul d  be  he miz y g o us  i n males  a n d  heter oz y g o us  i n fe males. 
1 0.  Recessi ve i n herita nce i ncl u des b ot h a ut os o mal a n d X -li n ke d recessi ve c o n diti o ns. F or X-li n ke d 
recessi ve c o n diti o ns,  rele va nt varia nts  w o ul d  be  e x pecte d t o be  he miz y g o us  i n males  a n d  h o m oz y g o us  or 
c o m p o u n d heter oz y g o us i n  fe males. 
 
N G S - N B S a n d A d diti o nal Ge n o mic Fi n di n gs 
I n t he “ Well- C hil d” c o h ort t here will be n o p he n ot y pe t o i nf or m a dia g n ostic list. I n 
a d diti o n, all c o n diti o ns u nrelate d t o t he p he n ot y p e k n o w n f or patie nts i n t he “ Dia g n ose d 
C o h ort” w o ul d be c o nsi d ere d “i n ci de ntal” t o t heir pri mar y i n dicati o n f or se q ue nci n g. 
T heref ore, t he a nal ysis of t he N G S - N B S list a n d a d diti o nal ge n o mic fi n di n gs will be 
m ore a ki n t o scree ni n g t ha n dia g n ostic testi n g.  I n t his setti n g, t he pri or pr o ba bilit y t hat 
a n i n di vi d ual has a rare Me n delia n dis or der will be ver y s mall ( bas e d o n t he p o p ulati o n 
pre vale n ce of t h e dis or der), a n d t h us t he p ositi ve pre dicti ve val ue of ge n o mic i nf or mati o n 
will be str o n gl y i nfl ue nce d b y t he s pecifi cit y of t he res ults. B ot h t he “ Dia g n ose d C o h ort” 

 
a n d “ Well -C hil d C o h ort” will recei ve res ults fr o m t he “ N G S -N B S” ge n e list. I n or der t o 
mi ni mize false p ositi ves, we will use stri n ge nt crit eria f or ret ur n of res ults a n d will o nl y 
ret ur n vari a nts t hat are d ee me d t o be “ p at h o ge nic” or “li kel y pat h o ge nic” a n d c o nsiste nt 
wit h t he e x pecte d i n h erita nce p atter n of t he c o n diti o n (e g. h o m oz y g o us or pres u me d 
c o m p o u n d heter oz y g o us varia nts i n t he cas e of a recessi ve c o n diti o n). 
 
Varia nts will be c o m p utati o nall y selecte d f or t heir prese nce i n a ge n e o n t h e N G S -N B S 
list, t heir li kel y pat h o ge nic si g nifica nce a n d, i n t he case of recessi ve c o n diti o ns, w het her 
o ne or t w o m utati o ns are prese nt ( 3 4). Gi ve n t he lar ge n u m ber of p ossi ble ge n o mic 
fi n di n gs, a n d t he l o w a pri ori li keli h o o d t hat i n di vi d uals i n t he “ Well- C hil d” c o h ort 
w o ul d be aff ecte d wit h a n y gi ve n rare ge netic dis or der, it will be critical t o stri ke a 
bala nce  b et wee n t he “se nsiti vit y” a n d t he “s pecificit y” of t he a nal ysis s o as t o c orrectl y 
i de ntif y i n di vi d uals at hi g h ris k f or a treata ble g e netic c o n diti o n wit h o ut o ver w hel mi n g 
t he m olec ular a n al ysts, M G L, a n d cli nicia ns wit h lar ge n u m bers of varia nts of u ncertai n 
si g nifica nce. T his a n al ysis will utilize t he sa me c o m p utati o nal classes as descri be d i n 
Ta ble 1, wit h a d diti o nal i nf or matic filteri n g t o det er mi ne w hic h varia nts q u alif y f or 
h u ma n re vie w.  We will r e vie w vari a nts t hat satisf y t he f oll o wi n g c o n diti o ns: 
1)  F or ge n es ass o ciate d wit h c o n diti o ns i n herite d i n a d o mi na nt fas hi o n, w e will 
re vie w a n y v aria nts i n c o m p utati o nal classes A a n d B;  
2)  F or ge nes ass ociat e d wit h c o n diti o ns i n herite d i n a recessi ve fas hi o n, we will 
re vie w varia nts i n cases w here t w o or m ore varia nts fr o m c o m p utati o nal  classes 
A, B, or C are pr ese nt.  
 
Cases f ulfilli n g t hese crit eria will u n der g o re vie w b y a m olec ular a nal yst a n d t he 
m olec ular si g n - o ut c o nf ere nce, a n d o nl y vari a nts deter mi ne d t o be “ k n o w n pat h o ge nic” 
or “li kel y pat h o ge nic” a n d c o nsiste nt wit h t he e x pecte d i n herita n ce p atter n w o ul d be 
ret ur ne d i n t he c o nte xt of N G S-N B S.  All ot her cases will be re p orte d as “ n e gati ve.” 
T his a p pr oac h is a n i n h er e ntl y c o nser vati ve o n e. We rec o g nize t h at t he strict t hres h ol ds 
o utli ne d a b o ve will i n her e ntl y ha ve i m perfect se nsiti vit y f or detecti n g cli nicall y rele va nt 
varia nts, b ut at t he sa me ti me t his a p pr oac h will ha ve hi g her s pecificit y a n d t heref ore 
pr otect a gai nst f alse p ositi ve res ults. T his is als o a pra g matic a p pr oac h, si nce it will be 
i m p ossi ble f or a h u ma n t o c o m pre he nsi vel y re vie w eac h of t he ma n y varia nts t hat will be 
i de ntifie d i n e ver y i n di vi d ual.  T h us, t he bala nce we are stri vi n g t o ac hie v e is t o 
ma xi mize cli nical se nsiti vit y a n d s pecificit y, w hile mi ni mizi n g t he eff ort re q uire d of a 
h u ma n m olec ular  a n al yst. 
 
C LI A  C o nfir m ati o n:  
All res ults dee me d r e p ort a ble i n t he N C N E X U S st u d y will be c o nfir me d b y ort h o g o nal 
met h o ds ( Sa n ger se q u e nci n g) i n t he C LI A- certifie d U N C H os pitals M G L ( M ol Ge n 
C ust o m D N A Se q ue nci n g, see A p pe n di x 7). A cli nical re p ort will be g e nerate d a n d 
a p pr o ve d b y a b oar d- certifie d m olec ular ge neticist or pat h ol o gist. T his res ult will be 
pr o vi de d t o t he par e nts a n d will be eli gi ble t o be i ncl u de d i n t he electr o nic healt h 
rec or d ( N C N E X U S N G S-N B S Electr o nic Me dical Rec or d ( E M R): A p p e n di x 2 0 a n d 
N C N E X U S A d diti o nal Res ults Electr o nic Me dical Rec or d ( E M R) C o nse nt: A p pe n di x 
2 1). 

 
 
R a n d o mi z ati o n:  
After se q u e nci n g a n d a nal ysis of t he i n dicati o n- base d a nal yses a n d/ or N G S- N B S 
are c o m plet e, t he c o u ple will be ra n d o mize d i nt o a “ decisi o n gr o u p” or a “c o ntr ol 
gr o u p”. T he c o u ple will be c o ntact e d t o arra n ge a ret ur n of res ults visit wit h a 
ge neticist a n d ge netic c o u nsel or.  
 
Ra n d o mizati o n will be c o m p uter i m ple me nte d usi n g per m utate d bl oc k 
ra n d o mizati o n wit h bl oc ks of ra n d o ml y var yi n g size. Partici pa nts will be stratifie d 
f or bl oc k ra n d o mizati o n base d o n t hree para meters: st u d y c o h ort (“ Dia g n ose d 
C o h ort” or “ Well- c hil d C o h ort”), la n g ua ge prefere nce (“ E n glis h” or “ S pa nis h”), 
a n d t he relati o ns hi p stat us of t he pare nt(s) gi vi n g c o nse nt (“ Si n gle” or “ C o u ple”). 
I n t his wa y, we will ac hi e ve o pti m u m ra n d o mizati o n wit hi n eac h of t hese gr o u ps. 
 
T h ose i n t he “ decisi o n gr o u p” will be gi ve n i nf or mati o n a b o ut t his visit a n d f ut ure 
st u d y acti vities. I n a d diti o n, t he y will als o be gi ve n access t o a s u p ple me nt t o t he 
electr o nic d ecisi o n ai d t hat e x plai ns t he t hree cate g ories of a d diti o nal ge n o mic 
fi n di n gs (a d ult- o nset me dicall y acti o na ble, c hil d h o o d- o nset n o n-me dicall y 
acti o na ble, a n d carrier st at us), a n d h o w s uc h i nf or mati o n mi g ht be of p ote ntial 
be nefit or ha r m. T he y will be a ble t o deci de w hic h cate g ories of a d diti o nal fi n di n gs 
t o lear n (all, n o ne, or a n y c o m bi nati o n of s o me of t he cate g ori es). We will 
e nc o ura g e pare nts t o use t he ai d at h o me pri or t o t he ret ur n of res ult visit. D uri n g 
t he visit, t he y will have t he o p p ort u nit y t o disc uss t he i nf or mati o n a b o ut t he 
cate g ories fr o m w hic h t h e y ca n re q uest res ults a n d h o w t o c o m m u nicate t h eir 
decisi o ns a b o ut re q uesti n g cate g ories of a d diti o nal ge n o mic i nf or mati o n. T he y will 
be as ke d t o si g n a f or m t hat d oc u me nts w hic h cate g ories of res ults t he y ha ve 
re q ueste d. 
 
T he “c o ntr ol gr o u p ” will n ot ha ve t he o pti o n t o re q uest t he “a d diti o nal ge n o mic 
fi n di n gs” a n d will n ot recei ve access t o t he s u p ple me nt t o t he electr o nic d ecisi o n 
ai d. T he y will o nl y recei ve i nf or mati o n a b o ut t he u pc o mi n g ret ur n of res ult visit. 
 
R et ur n of R e s ult s  Vi sit:  
Q ualifie d ge netic pr ofessi o nals ( p h ysicia ns a n d ge netic c o u nsel ors) w h o are part of 
t he researc h tea m will meet wit h t he c o u ples after se q ue nci n g is c o m plete t o 
discl ose cli nicall y c o nfir me d v aria nts t hat meet a hi g h bar f or e vi de nce of 
pat h o ge nicit y. T his f or m of ret ur n of res ults acc o m pa nie d b y c o m pre h e nsi ve 
ge netic c o u nseli n g is t he g ol d sta n dar d i n ge netic t esti n g, a n d will be c o m ple me nte d 
b y pare ntal utilizati o n of t he decisi o n ai d a n d ge n etic c o u nseli n g d uri n g t he first 
st u d y visit. Ne gati ve res ults will be acc o m pa nie d b y a disc ussi o n of t he li mitati o ns 
of N G S - N B S, esse ntiall y c o m m u nicati n g t he ca v eat t hat a ne g ati ve res ult d oes n ot 
f ull y r ule o ut t he p ossi bilit y of a n y healt h c o n diti o ns de vel o pi n g i n t he f ut ure, as is 
t he case wit h a n y s cree ni n g test.  

 
I n cases w her e t he fa mil y ca n n ot ret ur n f or a n i n p ers o n visit, f or e xa m ple, if t he y 
ha ve m o ve d fr o m t he ar ea, we will ret ur n res ults b y tele p h o ne or S k y pe.  T he 
re p orts will be e maile d s ecurel y b ef ore t he call s o pare nts ca n re vie w it pri or t o o ur 
disc ussi o n.   
Cli nicall y c o nfir me d res ults will be s u m marize d b y a la b orat or y re p ort gi ve n t o t he 
c o u ple at t he visit. T he y will be as ke d w het her or n ot t he y c o nse nt t o ha vi n g t he 
res ults place d int o t he c hil d’s me dical rec or d a n d will si g n a f or m i n dicati n g t his 
decisi o n. A cli nical f oll o w -u p pla n f or all res ults will be esta blis he d wit h t he 
pare nts.  
 
Relati ves, pri maril y pare nts of c hil dre n i n t he dia g n ose d c o h ort, ma y be as ke d t o 
pr o vi de a sali va sa m ple t o hel p us i nter pret a v aria nt or c o m bi nati o n of vari a nts t hat 
ma y pr o vi de a n e x pl a nati o n f or t he c hil d's s y m pt o ms. I n t he case of recessi ve 
c o n diti o ns, li ke ma n y of t h ose teste d f or i n N C N E X U S, t here ma y b e t w o ge netic 
varia nts i de ntifie d b ut t h e la b orat or y t est ca n n ot t ell w het her t he y are eac h prese nt i n 
differe nt c o pies of t he g e ne (i n herite d se p aratel y fr o m eac h p are nt) or t o get her i n o ne 
c o p y of t he ge n e ( b ot h i n herite d fr o m t he s a me pare nt).  T his i nf or mati o n ca n be 
i m p orta nt i n deter mi ni n g w het her t he v aria nts t hat were d etecte d fit wit h a recessi ve 
i n herita nce p atter n f or t h e c o n diti o n.  I n ot h er cas es, t he la b orat or y ca n n ot 
i m me diatel y deter mi ne w het her a v aria nt is har mf ul or n ot. T hese vari a nts are calle d 
“ varia nts of u n cert ai n cli nical  si g nifica nce” ( V U S). A V U S res ult mea ns t h at a 
ge netic vari a nt was f o u n d, b ut t here is n ot e n o u g h i nf or mati o n a b o ut it t o k n o w f or 
s ure w het her it ca use dis ease or n ot. 
  
A n esti mate d 5 0 relati ves will be c o nse nte d bef ore a sa m ple is o btai ne d.  T he sa m ple 
will be la bele d wit h a N C N E X U S st u d y n u m ber.  W he n t he testi n g is c o m plete d, t he 
la b will re p ort t he res ults t o a certifie d g e netic c o u nsel or or me dical g e neticist o n t he 
researc h tea m b y a sec ur e e mail a n d t he y will re p ort t he res ults t o t he relati ve b y 
p h o ne. T he c hil d's cli nical re p ort will be a me n d e d t o i ncl u de t he i nf or mati o n lear ne d 
as a res ult of testi n g; h o we ver, t he relati ve will o nl y be i de ntifie d b y his or her 
relati o ns hi p t o t he partici pa nt a n d n ot b y na me.  P are nts will be c o u nsel e d t hat t he 
acc ur ac y of t he res ults de pe n ds u p o n k n o wi n g t he tr ue bi ol o gical relati o ns hi p of t he 
relati ves bei n g teste d a n d t hat if t he state d fat her of a partici p a nt is n ot t he tr ue 
bi ol o gical fat her, t he i nter pretati o n ma y be i n c orrect. 
 
 
S u bse q ue nt Ret ur n of A d diti o n al Res ults ( Decisi o n Gr o u p o nl y): 
Electi o n t o recei v e a n y a d diti o nal res ults will tri g ger a n i n de p e n de nt a n al ysis of  
ge n o mic data a n d C LI A c o nfir mati o n.  C o u ples re q uesti n g res ults fr o m t he carri er 
stat us cate g or y 
will be a ble t o lear n t hes e res ults d uri n g a sc h e d ule d p h o ne call wit h a ge netic 
c o u nsel or. 
Re q uests f or t he ot her t w o cate g ories will tri g ger a sec o n d ret ur n of res ults visit 
wit h a ge neticist a n d ge n etic c o u nsel or. C o u ples i n t he “ decisi o n gr o u p ” will be 
as ke d t o c o m plete a brief p ost -decisi o n  q uesti o n naire (t he Ti me 2 A q u esti o n naire) 
after t he y d eci de w het her or n ot t o re q uest a d diti o nal ge n o mic fi n di n gs t o assess 

 
t he c o nse q ue n ces of h a vi n g t his o pti o n. 
 
F oll o w -u p  Q u e sti o n n air e s:  
All partici pa nts will c o m plete t w o f oll o w u p q uesti o n naires f oll o wi n g t he ret ur n of 
res ult visit; a Ti me 3 q uesti o n naire c o m plete d wit hi n 2 wee ks of t he visit a n d a 
Ti me 4 q uesti o n naire c o m plete d 3 m o nt hs after t he visit. B ot h will assess t he 
s h ort- a n d l o n ger- ter m c o nse q ue nces of decisi o n- ma ki n g a n d res ults discl os ure.  
 
C o u ples w h o d o n ot c o m plete a q uesti o n naire i n a ti mel y ma n ner ma y be offere d 
t he o pti o n of c o m pleti n g q uesti o n naires i n a tele p h o ne i nter vie w. Q u esti o n naires 
will be a d mi nistere d i n Q ualtrics, accesse d via a c o m p uter or m o bile de vice, wit h 
pa per a n d p e ncil versi o ns of t he q uesti o n naires a vaila ble t o t h ose w h o prefer n ot 
t o c o m plete t he m o nli ne. 
 
F oll o w -u p  pr o c e d ur e s  
 
Re vise d  res ults:  
A d va nce m e nts i n me dical ge netics a n d o ur u n d ersta n di n g of varia nt pat h o g e nicit y 
will c o nti n u o usl y e v ol ve a n d t h us i m pact t he cli nical i nter pretati o n of varia nts 
i de ntifie d i n t he st u d y partici pa nts. O ne sce n ari o t hat ca n be a ntici pate d is t hat t he 
pat h o ge nicit y assess me nt f or a partic ular v aria nt ma y c ha n ge o v er ti me. T his 
mea ns t hat t he i nitial classificati o n of a varia nt ma y be s u perse d e d b y a s u bse q ue nt 
reclassificati o n. T his c o ul d mea n t hat a res ult t hat was pre vi o usl y “ n e gati ve” c o ul d 
c ha n ge t o “ p ositi ve” if a varia nt i nitiall y classifie d as V U S is reclassifie d as 
pat h o ge nic. It is als o p ossi ble t hat a varia nt i nitiall y  classifie d as “ p at h o ge nic” or 
“li kel y pat h o ge nic” w o ul d be recl assifie d t o V U S. I n t his sce nari o t he pre vi o us 
“ p ositi ve” res ult c o ul d c h a n ge t o “ ne g ati ve.” T h es e t y pes of re vis e d res ult will be 
c o m m u nicate d t o partici p a nts wit h o ut n otificati o n of t he  F D A.  
 
I n a d diti o n t o t he e x pecte d reclassificati o n of vari a nts, t here are ot her t y pes of 
re vise d res ults t hat we ca n a ntici pate. O ver ti me t he ass ociati o n of m ore ge n es wit h 
diseases a n d t he d e vel o p me nt of pre ve nti o n or treat me nt will res ult i n reassi g n me nt 
of l oci a n d lea d t o c h a n g es i n t he i nter pretati o n of se q ue nci n g res ults. I n a d diti o n, 
a d va nce me nts i n se q ue nci n g tec h n ol o g y, bi oi nf or matics a nal ysis, a n d vari a nt 
assess me nt will i n here ntl y necessitate p eri o dic alt erati o ns of t he est a blis he d 
a nal ytic pi peli nes. A m o n g t he maj or researc h acti vities of t he N C N E X U S pr oject 
will be t he refi ne m e nt of t he ge nes/l oci t hat are assi g ne d t o eac h cate g or y of 
ge n o mic i nf or mati o n (as defi ne d a b o v e), e v al uati o n of ne w bi oi nf or matics 
al g orit h ms, a n d t he criteria use d t o assess pat h o ge nicit y of varia nts. 
 
•  
A d va nce m e nts i n t he scie nce of m e dici ne will c o nti n u o usl y a d d t o 
o ur k n o wle d ge of t h e ge n etic u n der pi n ni n gs of dis ease. Alt h o u g h 
m ost of t he i n b or n err ors of meta b olis m t hat will be prese nt i n t he 
“ dia g n ose d c o h ort” ha v e defi niti vel y esta blis he d ge netic eti ol o gies 
(e g. P K U, M C A D D), ot h er c o n diti o ns re prese nte d i n t his c o h ort (e g. 
heari n g l oss) are still s u bject t o acti ve i n vesti gati o n. T heref ore, t he 

 
dia g n ostic lists utilize d f or t he “i n dicati o n -b ase d a nal ysis” will be 
u p date d peri o dicall y t o i ncl u de ne wl y disc o vere d ge nes, w he n t h e 
researc h tea m dee ms t h ose disc o veries t o ha v e s ufficie nt cli nical 
vali dit y. Si milarl y, ne w treat me nts a n d ma n a ge me nt strate gies will 
be defi ne d f or ma n y ge n etic c o n diti o ns, t h us c ha n gi n g t heir 
p ote n tial cli nical acti o na bilit y. T heref ore, t h e list of ge nes t hat 
c o nstit utes t he “ N G S - N B S” ma y be u p date d t o acc o u nt f or s uc h 
a d va nce me nts. Fi nall y, n e wl y disc o vere d ge netic c o n diti o ns will be 
re vie we d a n d assi g ne d t o ot her cate g ories of g e n o mic i nf or mati o n 
(a d ult- o nset me dicall y acti o na ble, c hil d h o o d- o nset n o n-me dicall y 
acti o na ble, a n d carrier st at us) as  a p pr o priate. 
 
•  
A d va nce m e nts i n c o m p utati o nal pr ocessi n g a n d a n al ysis of N G S 
data will c o nti n u o usl y i m pr o ve t he a n al ytic vali dit y of varia nt 
calli n g pi peli nes , i m pr o vi n g t he se nsiti vit y a n d s pecificit y of t he 
varia nts t hat are i de ntifie d. T heref ore, w e will utilize t he ra w 
se q ue nce d ata ge n erate d t hr o u g h t he N C N E X U S pr oject (a n d ot h er 
o n g oi n g pr ojects at U N C) t o e val uate n e w i nf or m atics pi peli nes.  
T hese a n al y ses will be perf or me d i n parallel wit h t he esta blis he d 
pr oce d ur es descri be d a b o ve, a n d o nl y w he n t he res earc h t ea m 
i de ntifies s u bsta ntiall y i m pr o ve d perf or ma nce will t he pi peli nes 
descri be d i n secti o n 2 be u p date d. 
 
•  
O pti mizi n g t he criteria f or a nal ysis a n d  re p orti n g of ge n o mic 
varia nts i n t he c o nte xt of N G S- N B S is a c ore researc h q uesti o n f or 
t he N C N E X U S pr oject, a n d t h us defi ni n g t he m ost effecti ve 
i nf or matics al g orit h ms is e x pecte d t o b e a n o n g oi n g tas k. F or 
e xa m ple, o ne g o al of t he researc h pr oj ect is t o i n vesti gate 
i nf or matics al g orit h ms t hat ca n be us e d t o select v aria nts f or h u ma n 
re vie w, o pti mizi n g t he cli nical se nsiti vit y a n d cli nical s pecificit y 
w hile mi ni mizi n g h u ma n w or kl oa d. T heref ore, w e will utilize t he 
varia nt data g e nerate d t hr o u g h t he N C N E X U S pr oject (a n d ot her 
o n g oi n g pr ojects at U N C) t o e val uate t hes e al g orit h ms, i n parallel 
wit h t he pr oce d ures descri be d a b o ve. O ne e x a m ple will be t he 
de vel o p me nt of al g orit h ms t hat ca n e val uat e vari a nt a n n otati o ns i n 
or der t o satisf y s pecific criteria f or  p at h o ge nicit y assess me nt, i n 
or der t o  pr o vi de a m ore acc urat e preli mi nar y classificati o n t ha n t he 
c o m p utati o nal classifier descri be d i n Ta bl e 1.  T h e al g orit h ms will 
be u p date d o nl y w h e n t he researc h tea m is satisfie d t hat a n u p date d 
i nf or matics al g orit h m is s u peri or. 
 
If, as a res ult of a n y of t he a d va n ce me nts des cri be d i n t he b ullets a b o ve, t he 
researc h tea m deter mi nes t he nee d t o u p date g e ne lists, bi oi nf or matics pi peli nes, 
varia nt a nal ysis al g orit h ms t he F D A will be pr o vi de d a 5 - da y n otice. All 
partici pa nts a nal y ze d usi n g t he pre vi o us versi o n of t he pr ot oc ol will ha ve t heir data 
rea nal y ze d, a n d i n t he e v e nt t hat a n y ne w fi n di n gs q ualif y f or ret ur n of res ults, 

 
t he y will be c o nfir me d i n t he M G L. Pare nts will be re-c o ntact e d t hat t he res ults 
t he y ha ve r ecei v e d d uri n g t he st u d y ha ve c ha n g e d as a res ult of rea n al ysis. 
 
T h us,  b y  desi g n  t h ere  will  be  d e vel o p me nt al  c ha n g es  i n  t he  pr ot oc ol,  
acc o m pa ni e d b y p eri o di c rea nal ysis of t he N G S data, wit h t he p ossi bilit y t hat 
t he res ults of t he a n al ysis ma y c h a n ge o ver ti me a n d s o me p artici pa nts will be 
re-c o nt acte d f or  u p date d 
res ults.  T his sit uati o n will be clearl y des cri be d i n t he i nf or me d c o nse nt. 
 
L o n git u di n al f oll o w -u p of  r e s ult s: 
T he d o w nstrea m i m plicati o ns of p ositi ve res ults are of great i nterest f or t he N C 
N E X U S  pr oject. We will t heref ore pla n t o e n g a ge i n l o n git u di nal f oll o w- u p f or t he 
d urati o n of t he st u d y (as l o n g as f u n di n g all o ws).  T his f oll o w- u p will i ncl u de b ot h 
cli nical f oll o w- u p a n d ps yc h os ocial e val u ati o ns of pare nts.  
 
4   Cli ni c al f oll o w -u p  
T he cli nical f oll o w- u p of partici pa nts i n t he N C N E X U S st u d y will de pe n d o n t he 
c o h ort t o w hic h t he y bel o n g a n d t he t y pe of res ult t he y recei ve. 
 
•  Previ o usly k n o w n di a g n oses: Partici pa nts fr o m t he “ Dia g n ose d c o h ort” 
will alrea d y ha v e esta blis he d sta n dar d - of-care f oll o w- u p t hr o u g h t he 
s pecialt y cli nics fr o m w hic h t he y are recr uite d, a n d t heir partici pati o n i n t he 
st u d y will ha ve n o i m pact o n t his o n g oi n g cli nical care. R es ults will be 
pr o vi de d t o t he par e nts b y a certifi e d ge netic c o u nsel or a n d M D me dical 
ge neticist, a n d c o m m u nicate d t o t heir cli nical pr o vi ders via sec ure 
messa gi n g. A n y varia nts t hat are c o nfir me d i n t he C LI A la b will be eli gi ble 
f or place me nt i n t he E H R. T he fi n di n gs ma y be utilize d t o g ui de care, b ut 
t his w o ul d be e ntirel y at t he discreti o n of t he esta blis he d cli nical pr o vi ders.  
I n t his case, cli nicia ns ass ociate d wit h t he N C N E X U S st u d y will ser ve as 
c o ns ultati ve res o urces f or cli nical pr o vi ders b ut will n ot direct t he care of 
t he patie nts. St u d y pers o n nel will acti vel y m o nit or t he E H R as part of a n 
o bser vati o nal st u d y t o trac k h o w ge n o mic fi n di n gs are utilize d.  
 
•  Previ o usly u n k n o w n di a g n oses: Partici pa nts i n b ot h t he “ Well -c hil d 
c o h ort” a n d “ Dia g n ose d c o h ort” will ha ve t he p ot e ntial t o recei v e p ositi ve 
fi n di n gs fr o m 
N G S - N B S or ot her a d diti o nal cate g ori es of ge n o mic i nf or mati o n t hat will 
re pres e nt ne w i nf or mati o n (i.e. u nrelat e d t o a dia g n ostic i n dicati o n). T hese 
res ults will be pr o vi de d t o pare nts b y a certifie d g e netic c o u nsel or a n d M D 
me dical ge neticist, a n d a sta n dar d - of-care cli nical f oll o w - u p pla n will be 
esta blis he d t hat is a p pr o priate f or t he fi n di n g. T his c ust o mize d pla n ma y 
i n v ol ve l o n g-ter m m o nit ori n g b y a pe diatrici a n, dia g n ostic i ma gi n g, ot her 
scree ni n g tests, a n d referral t o s pecialists.  T his f oll o w- u p pla n will be part 
of t he patie nt’s cli ni cal care. Cli nicia ns ass ociat e d wit h t he N C N E X U S 

 
st u d y will ser ve as c o ns ultati ve res o urces f or cli nical pr o vi ders b ut will n ot 
be directl y r es p o nsi ble f or t he care of t he p atie nts. St u d y pers o n nel will 
acti vel y m o nit or t he E H R as part of a n o bs er vati o nal st u d y t o trac k h o w 
ge n o mic fi n di n gs are utilize d.  I n or d er t o miti gate me dical ris ks i n t his 
p o p ulati o n, st u d y pr o vi ders will deter mi ne s pecifi c be nc h mar ks ( de p e n di n g 
o n t he i n di vi d ual fi n di n g) t hat will be e val uate d t o e ns ure t hat a p pr o priate 
f oll o w- u p is bei n g gi ve n. St u d y pers o n nel will trac k t hese be n c h mar ks a n d, 
if a be nc h mar k is n ot met, we will c o m m u nicate wit h t he pare nt t o 
deter mi ne w h y a n d t o d e vel o p a n alter n ati ve cli nical f oll o w- u p pla n 
de pe n di n g o n t he sit uati o n. 
 
•  Ne g ative res ults: M ost parti ci pa nts i n t he “ Well -c hil d c o h ort” a n d s o me 
partici pa nts i n t he “ Dia g n ose d c o h ort” will ha v e ne gati ve fi n di n gs.  Res ults 
will be pr o vi de d t o pare nts b y a certifie d g e netic c o u nsel or a n d M D 
me dical ge neticist, pare nts will be c o u nsele d re g ar di n g t he s mall c ha nce of 
a false n e gati ve r es ult, a n d t he patie nts will u n der g o r o uti ne cli nical f oll o w -
u p wit h t heir pr o vi ders. St u d y pers o n nel will passi vel y m o nit or f or rare 
cases of false ne g ati ve ge n o mic res ults b y i n viti n g pare nts t o c o ntact t he 
st u d y i n t he rare e v e nt t hat s y m pt o ms of a ge netic dis or der de vel o p i n t heir 
c hil d. 
 
O utc o mes will be trac k e d i n e ver y partici pa nt b y wa y of a c hart re vie w p erf or me d 
at t he e n d of t he st u d y peri o d. T his re vie w will i ncl u de de vel o p me ntal o utc o mes, 
cli nical e ve nts s pecific t o a n y dia g n oses, a n d res ults of a n y scree ni n g or 
dia g n ostic tests.  
 
I n di c ati o n-b a s e d  r e a n al y si s: 
All pare nts i n t he st u d y will be gi ve n a n o p p ort u nit y t o re q uest a n “i n dicati o n-
base d a nal ysis” s h o ul d s y m pt o ms of a ge netic dis or der arise i n t heir c hil d. We 
a ntici pate t hat s uc h r e q uests will be rare. If a re q uest is ma de, a n a p pr o pri ate 
dia g n ostic list will be de vel o pe d ( de p e n di n g o n t he c hil d’s s y m pt o ms) a n d 
m olec ular a n al ysis will be perf or me d i n acc or d a nce wit h secti o n 2 a b o ve. R es ults 
will be c o nfir me d i n t h e C LI A la b a n d pr o vi de d i n acc or d a nce wit h secti o n 2 
a b o ve. 
 
S c h e d ul e of  a cti viti e s  
T he sc he d ule of acti vities is s h o w n i n t he St u d y Desi g n Sc he matic a b o ve 
 
T he e nr oll me nt tele p h o n e call will ta ke a n esti mate d 1 5 mi n utes t o re vie w t he 
pare nts’ partici pati o n c o nse nt f or m a n d sc h e d ule Visit 1. 
 
•  Visit 1 will ta ke a n esti mate d 3 0 mi n utes i n or der t o all o w pare nts t o 
ha ve a n y q u esti o ns a ns w ere d a n d m a ke a fi nal decisi o n a b o ut w het her 
or n ot t o acce pt N G S- N B S f or t heir c hil d. We e x p ect t hat t his e nc o u nter 
will be  facilitate d b y t he pare nts ha vi n g access t o t he electr o ni c decisi o n 

 
ai d pri or t o t he visit.  
 
•  Visit 2 will occ ur a p pr o xi matel y 3 - 4 m o nt hs after Visit 1.  F or m ost 
partici pa nts i n t he “ Dia g n ose d C o h ort” t he ret ur n of res ults is li kel y t o ta ke 
3 0 mi n utes t o re vie w t he i n dicati o n- base d a n al ysis. F or > 9 5 % of 
partici pa nts i n t he “ Well - C hil d C o h ort” t he ret ur n of res ults is li kel y t o ta ke 
1 5 mi n utes or less f or ne gati ve res ults, w hereas f or t he s mall n u m ber t hat d o 
ha ve a p ositi ve fi n di n g t h e ret ur n of res ults c o ul d t a ke 3 0- 4 5 mi n utes t o 
pr o vi de c o nte xt ualize d i nf or mati o n a n d rec o m me n d a f oll o w- u p pla n.  F or 
t he t w o-t hir ds of partici p a nts ra n d o mize d t o  t he “ decisi o n gr o u p” w e 
esti mate t hat 3 0 mi n utes will be nee de d t o re vie w a n y q uesti o ns t he pare nts 
ha ve a b o ut t he a d diti o nal cate g ories of ge n o mic i nf or mati o n t hat t he y ma y 
deci de w h et her or n ot t o lear n. 
 
•  Visit 3 will occ ur a p pr o xi matel y 1 - 2 m o nt hs after Visit 2. T he le n gt h of t he 
visit will de pe n d o n h o w ma n y cate g ori es of a d diti o nal i nf or mati o n are 
re q ueste d. We pr e dict t hat t he m ost t y pical res ult will be p ositi ve carrier 
stat us f or 1- 4 c o n diti o ns a n d ne gati ve fi n di n gs f or t he ot her t w o cat e g ories 
(a d ult- o nset me dicall y acti o na ble, c hil d h o o d- o nset n o n-me dicall y 
acti o na ble). F or t his t y pe of visit we esti mate 3 0 mi n utes f or ret ur n of 
res ults. I n t h e rare e v e nt of a p ositi ve fi n di n g i n t he a d ult-o nset me dicall y 
acti o na ble or c hil d h o o d- o nset n o n- me dicall y acti o na ble cat e g ories w e 
w o ul d e x pect t he visit t o last 6 0 mi n utes or m ore if nee d e d.  
 
5 
St u d y o ut c o m e  e v al u ati o n s  
 
Pri mar y O utc o me Meas ure:  
 
    Pare ntal Decisi o n Ma ki n g Usi n g Decisi o n Ai d.   [ Ti me Fra me: a vera ge of 3- 6 m o nt hs.] 
 
    A nal ysis of pare nts' d ecisi o ns after t he y c o m plete a n o n-li ne decisi o n ai d t o see if t he y 
wis h t o partici pate i n t he st u d y. Pare nt partici pa nts ra n d o mize d t o t he decisi o n gr o u p, 
after t heir c hil d is se q ue n ce d, ma y deci de w h at, if a n y, a d diti o nal cate g ories of c o n diti o ns 
t he y wis h t o lear n a b o ut. O pti o ns will be yes, n o, or u ns ure. 
 
    Se nsiti vit y of W h ole E x o me Se q ue nci n g i n Det ecti n g C o n diti o ns b y C o m pari n g 
Res ults of Se q ue nci n g t o t he A p pr o priate Ge nes Ass ociate d Wit h t he C hil d's U n derl yi n g 
C o n diti o n.   [ Ti me Fra m e: a p pr o xi matel y 3- 6 m o nt hs after D N A sa m ple o btai ne d.] 
 
    I n v esti gat ors will a nal yze se q ue n ci n g res ults i n t he dia g n ose d c o h ort t o deter mi ne t he 
a bilit y of w h ole e x o me s e q ue nci n g t o detect pat h o ge nic varia nts i n ge n es relate d t o 
p he n ot y pe. 
 
Sec o n dar y O ut c o me Meas ures:  
 

 
    Partici pa nt C haract eristics a n d Reacti o ns t o t he St u d y Will be C ollecte d T hr o u g h 
S ur ve ys.   [ Ti me Fra me:  Baseli ne a n d 3 m o nt hs after fi nal ret ur n of res ults visit.] 
 
    S ur ve ys are a d mi nistere d at Ti me 1 ( bas eli ne), after pare nt partici pa nts d eci de t o j oi n 
p hase I of t he st u d y, w hi c h i n v ol ves a greei n g t o vie w t he o nli ne decisi o n ai d a b o ut Ne xt-
Ge ner ati o n Se q ue nci n g Ne w b or n Scree ni n g ( N G S- N B S); at Ti me 2, after pare nt 
partici pa nts ha ve vi e we d t he decisi o n ai d a n d ma d e a decisi o n a b o ut acce pti n g N G S- N B S 
f or t heir c hil d ( y es/ n o/ nee d m ore i nf or mati o n; n ot e t hat t he ti mi n g is varia ble, de pe n di n g 
o n w he n partici pa nts c o m plete t his tas k, b ut ma y ra n ge fr o m h o urs t o wee ks); at Ti me 2a 
(f or pare nt partici p a nts ra n d o ml y assi g ne d t o lear n/ ma ke decisi o ns a b o ut a d diti o nal 
i nf or mati o n), after par e nt partici pa nts ha ve m a de t he decisi o n t o acce pt n o n e, s o me, or all 
cate g ories of a d diti o nal i nf or mati o n ( n ote t hat t he ti mi n g is varia ble de pe n di n g o n w he n 
pare nt partici pa nts c o m plete t his tas k, b ut occ urs after ret ur n of N G S- N B S res ults); Ti me 
3, w hic h occ urs 2 wee ks after ret ur n of N G S- N B S res ults; a n d Ti me 4, w hic h occ urs 3 
m o nt hs after Ti me 3.  
 
St u d y  e n d p oi nts  
 
Pri m ar y O bjecti ve 1: S cie ntific e n d p oi nts f or t his o bjecti ve will be a.) g e nerati o n 
of w h ole e x o me s e q ue nce data a n d v aria nt call files, b.) a nal ysis of v aria nts t o 
deter mi ne w het h er a n y disease -ca usi n g vari a nts e xist, c.) c o nfir mati o n of a n y 
s us pecte d vari a nts i n t he C LI A la b orat or y as a meas ure of a nal ytic vali dit y, a n d 
d.) c o m paris o n wit h cli nical data t o e v al uate t he s e nsiti vit y a n d s pecificit y of 
se q ue nci n g. 
 
Pri m ar y O bjecti ve 2: S cie ntific e n d p oi nts f or t his o bjecti ve will be a.) c urati o n of 
ge ne- disease pairs t o defi ne cli nical acti o na bilit y, b.) deter mi nati o n of a n 
acti o na bilit y t hres h ol d f or i ncl usi o n i n t he N G S- N B S ge ne list a n d defi niti o n of t he 
cate g ories of a d diti o nal g e n o mic i nf or mati o n, c.) ret ur n of res ults a n d o bs er vati o nal 
st u d y of patie nt o utc o mes a n d i nte grati o n of ge n etic fi n di n gs i nt o cli nical care. 
 
Pri m ar y O bjecti ve 3: S cie ntific e n d p oi nts will occ ur w h e n pare nts c o nse nt t o: a.) 
partici pate i n t he N C N E X U S st u d y b.) recei ve ge netic se q ue nci n g res ul ts ( N G S-
N B S) f or t heir c hil d c.) if ra n d o mize d t o t he “ d ecisi o n gr o u p”, deci de w het h er t o 
recei v e res ults i n a d diti o n t o N G S- N B S. A n a d diti o nal e n d p oi nt will occ ur if 
cli nicall y si g nifica nt vari a nts are ret ur ne d t o p are nts.  T he fi nal e n d p oi nt will ta ke 
pl ace w h e n par e nts c o m plete a seri es of q ua ntitati ve meas ures t o assess a ra n ge of 
fact ors r elate d t o partici pati o n i n t he st u d y. Please refer t o t he list of st u d y meas ure 
i n N C N E X U S Pr oject 3 L o n git u di nal St u d y Meas ures: see A p p e n di x 1 9). 
 
S a m pl e si z e  d et e r mi n ati o n 
T his pr oject is o ne of a c o ns orti u m of NI C H D/ N H G RI – f u n de d “ N SI G H T” 
pr ojects. Gi ve n t hat t his is a n e x pl orat or y st u d y, a f or mal p o wer calc ul ati o n ca n n ot 
be perf or me d. We e x pect t o be a ble t o perf or m j oi nt a nal yses of data acr oss t he 
c o ns orti u m t o a d dress certai n q uesti o ns t hat ma y re q uire lar g er sa m ple size.  
 

 
I n a d diti o n, t he st u d y was desi g ne d t o a d dress t he E L SI ( Et hical, Le g al, a n d S ocial 
I m plicati o ns) researc h q u esti o ns relate d t o t he i m pact of N G S o n patie nts a n d t heir 
fa milies. Usi n g P A S S s oft ware, w e esti mate d t he statistical p o wer f or a m ulti ple 
re gressi o n m o del of m ot hers’ mea n s c ores pre dicti n g t he decisi o nal c o nflict scale 
wit h t w o pre dict or vari a bles (st u d y gr o u p [ well- a n d dia g n ose d-c hil d gr o u ps] a n d 
race/ et h nicit y [ Blac k, W hite, a n d His pa nic]) a n d 1 0 c o ntr ol varia bles (e. g., 
de m o gra p hics, healt h literac y, tr ust i n me dical c o m m u nit y) t hat acc o u nt f or 2 0 % of 
t he varia nce i n sc or es, ass u mi n g a p- val ue of 0. 0 5. We ass u me d t he s a m ple w o ul d 
be s plit e q uall y acr oss r acial/et h nic gr o u ps, c o nsiste nt wit h t he distri b uti o n i n o ur 
st u d y p o p ulati o n. If st u d y gr o u p a n d race/et h nicit y acc o u nt f or 2 % or m ore of t he 
varia nce aft er c o ntr olli n g f or t he ot her v aria bles, we will ha ve statistical p o wer of at 
least 8 2 %, i n dicati n g acce pta ble p o wer f or c o m paris o ns b y st u d y gr o u p a n d 
race/ et h nicit y. We als o e xa mi ne d p o wer f or detecti n g differe nces i n decisi o n t o 
scree n acr oss st u d y gr o u ps. We esti mate d p o w er f or a l o gistic re gressi o n c o m pari n g 
decisi o n t o scree n b et wee n t he t w o st u d y gr o u ps, ass u mi n g t he well- c hil d gr o u p has 
a p pr o xi matel y 7 0 % pr o b a bilit y of acce pti n g N G S- N B S ( base d o n o ur Fra gile X 
N B S st u d y) a n d usi n g a p- val ue of 0. 0 5. O n t h e b asis of t hese ass u m pti o ns, we 
w o ul d ha ve 8 3 % p o w er or hi g her t o detect at least a 1 2 % differe n ce i n pr o b a bilit y 
of a gre ei n g t o scree ni n g bet wee n t he t w o st u d y gr o u ps, w hic h c orres p o n ds t o a n 
o d ds rati o of 2. 0. 
 
O ut c o m e d at a a n d d at a  a n al y si s  
 
Pri m ar y O bjecti ve 1:  
A.  Ge ner ati o n of w h ole e x o me se q ue nce data: D atas ets will i ncl u de ra w F A S T Q 
s h ort rea d files, ali g ne d B A M files, an d V C F varia nt call files. Varia nts will be 
a n n otate d a n d d e p osite d i n a l ocal data b ase as d escri be d i n  secti o n 2. 
B.  A nal ysis of varia nts: C urate d cli nical si g nifica nce of i n di vi d ual varia nts will be 
st ore d i n t he a n n otate d d ata base. Fi nal cas e-le v el res ults (acc or di n g t o Ta ble 2) f or 
eac h  patie nt  will  be  rec or de d.   T y pes  of  m utati o ns  t hat  are  detecte d  will  be  
c haracteri ze d i n  a g gr e gat e.  
C.  C LI A c o nfir mati o n: Res ults fr o m N G S will be c o m pare d wit h Sa n ger res ults 
i n t he C LI A la b t o assess t he false p ositi ve rat e (a nal ytic s pecificit y) of N G S.  
D.  Cli nical se nsiti vit y a n d cli nical s pecificit y: Calc ulati o ns of test se nsiti vit y a n d 
s pecificit y will be perf or me d base d u p o n t he dia g n ostic res ult a n d t he cli nical 
f oll o w- u p. 
 
Pri m ar y O bj e cti v e 2:  
 
A.  Cli nical acti o na bilit y c ura ti o n: C urate d literat ure re vie w data f or eac h g e ne-
disease pair will be st or e d i n a R E D Ca p data bas e. Fi nal sc ores deter mi ne d b y 
t he bi n ni n g c o m mittee will be rec or d e d a n d a n al y ze d.  
B.  Defi niti o n of cate g ories of ge n o mic i nf or mati o n: Base d o n c urati o n of a ge o f 
o nset a n d acti o na bilit y, t he bi n ni n g c o m mittee will deter mi ne t hres h ol ds t hat 
defi ne t he f o ur cat e g ories of ge n o mic i nf or mati o n as descri be d i n secti on 2. 
C.  O bser vati o nal st u d y of o utc o mes a n d i nte grati o n of fi n di n gs i nt o cli nical 

 
care: L o n git u di nal o utc o m es data will be c ollect e d i n a R E D Ca p data bas e 
a n d a nal yze d.  
 
Pri m ar y O bj e cti v e 3:  
C o nsiste nt wit h t he pri mar y res earc h q uesti o ns f or t his o bjecti ve, w hic h f o c us o n 
et hical use of N G S - N B S, we s pecif y t h e f oll o wi n g pri mar y i n de pe n d e nt varia bles: 
Race/et h nic it y ( n o n- His p a nic W hite, Blac k, His p a nic), healt h literac y, a n d c hil d 
stat us ( dia g n ose d vs. well). We s pecif y t he f oll o wi n g pri mar y de pe n d e nt varia bles: 
se q ue nci n g- r elate d distr ess, k n o wle d ge a b o ut N G S- N B S a n d (f or t he “ decisi o n 
gr o u p” o nl y) a b o ut a d diti o nal ge n o mic res ults (c o nti n u o us varia bles), decisi o n t o 
acce pt or decli ne N G S - N B S a n d (f or t he “ d ecisi o n gr o u p” o nl y) a d diti o n al 
ge n o mic res ults ( dic h ot o m o us varia bles), a n d d ecisi o nal c o nflict (a c o nti n u o us 
varia ble). Pri mar y a nal ys es will f oc us o n t hese o ut c o mes i n m ot hers. T hese 
a nal yses i n v ol ve a b et wee n - wit hi n desi g n a n d will be a nal yze d wit h mi xe d li near 
m o deli n g t o acc o m m o date nesti n g (i.e., assess me nts neste d wit hi n partici pa nts). 
M o dels wit h c o nti n u o us o utc o mes will be i m ple me nte d wit h S A S P R O C MI X E D 
beca use (a) it ca n ha n dle neste d data; ( b) it ha n dl es missi n g data m ore a p pr o priatel y 
t ha n re peate d- meas ures a nal ysis of varia nce, w hic h uses list wise deleti o n of 
missi n g data; a n d (c) it pr o vi des a wi der ra n g e of o pti o ns f or m o deli n g t he err or 
c o varia n ce str uct ure t ha n ge neral li near m o del pr o ce d ures, w hic h ass u me a n err or 
str uct ure t hat is ofte n u nr ealistic. M o dels wit h dic h ot o m o us o utc o mes will be 
i m ple me nte d usi n g mi xe d-effects l o gistic re gressi o n wit hi n S A S P R O C G E N M O D, 
w hic h s hares str e n gt hs si milar t o t h ose offere d b y P R O C MI X E D.  
 
6 
RI S K  A N A L Y SI S  
T he N C N E X U S res ear c h st u d y was la u nc he d i n res p o nse t o a re q uest fr o m NI H 
( NI C H D a n d N H G RI), t o perf or m researc h st u dies t o i n vesti gate ne xt- ge nerati o n 
se q ue nci n g st u dies i n ne w b or ns. Alt h o u g h s o me et hical g ui deli nes i n t he past ha ve 
raise d c o n cer ns a b o ut testi n g c hil dre n f or a d ult o nset c o n diti o ns, t here are fe w, if 
a n y, st u dies l o o ki n g at t he o utc o mes of s uc h testi n g. I n or der t o satisf y t he 
directi ves f or o bt ai ni n g a d diti o nal i nf or mati o n a b o ut t his, we ha ve pr o p ose d t he 
N C N E X U S st u d y t o pr o vi de researc h d ata t o be gi n t o a ns wer s o me of t h es e 
q uesti o ns. 
 
Pare nts e nr olle d i n t he st u d y will n ot be e x p ose d t o a n y si g nifica nt p h ysical or 
s ocial har ms. It is p ossi ble t hat t he y c o ul d e x p erie nce ps yc h ol o gical distress d ue 
t o ma ki n g decisi o ns a b o ut ha vi n g se q ue nci n g f or t heir c hil d, or deci di n g a b o ut 
w het her t o lear n certai n cate g ories of i nf or mati o n. O ne of t he o bjecti ves of t he N C 
N E X U S pr oject is t o st u d y precisel y t hese t y p es of i m pacts t hat mi g ht acc o m pa n y 
ge n o mic se q ue nci n g of n e w b or ns.  We esti mate t h at 8 0 % of t he fa mil y u nits will 
be c o u ples a n d 2 0 % will be si n gle pare nts, s o wit h e nr oll me nt of 4 0 0 c hil dre n i n 
t he st u d y we e x pect t o e nr oll 7 2 0 pare nts ( 4 0 0 fe male, 3 2 0 male).  T h e maj orit y 
will be bet wee n 2 0 -4 0 y ears of a g e.  
 

 
C hil dre n a n d ne w b or ns i n t he st u d y will be e x p ose d t o t he oretical p h ysical, s ocial, 
a n d ps yc h ol o gical har ms t hat ha ve bee n disc usse d a n d de bate d i n t he m e dical 
literat ure. A n a d diti o nal s o urce of ris k relates t o p ositi ve res ults ( b ot h tr ue p ositi ve 
a n d false p ositi ve) a n d false ne gati ve res ults.  A gai n, assess me nt of t he ma g nit u de 
of t hese p ote ntial ris ks is a maj or o verarc hi n g g o al of t he N C N E X U S pr oject. We 
esti mate t hat t he distri b uti o n of 4 0 0 c hil dre n a n d n e w b or ns a g es 0- 5 e nr olle d i n t he 
st u d y will be r o u g hl y 5 0 % fe male a n d 5 0 % male. 
 
A nti ci p at e d  Ri s k s  
P ote ntial ris ks t o w hic h t he s u bjects ( pare nts a n d t heir c hil dre n a n d ne w b or ns) 
will be e x p ose d as a res ult of t heir partici pati o n i n t he cli nical st u d y ca n be 
di vi de d bet wee n g e neric r is ks t hat are i n here nt t o h u ma n s u bjects ge netic 
researc h a n d ris ks t hat ar e s pecific a n d u ni q ue t o t he N C N E X U S pr oject. 
 
T he i n vesti gat ors ar e well a ware of g ui deli nes, o pi ni o ns, a n d ar g u me nts re g ar di n g 
ge netic testi n g i n c hil dre n f or a d ult- o nset c o n diti o ns ( 2, 6 a n d 3 8). Alt h o u g h 
c o ncer n h as bee n raise d r e gar di n g p ote ntial har ms ( v ul nera ble c hil d s y n dr o me, 
ge netic discri mi nati o n, pare ntal b o n di n g, a m o n g ot hers) t here has bee n a deart h of 
st u dies t hat ha ve trac k e d w het her t hes e act u all y occ ur. Use of ne xt ge n erati o n 
se q ue nci n g r aises t his t o a hi g her le vel of i m p orta nce. A d diti o nal res earc h i n t his 
area h as bee n rec o m me n de d b y sta ke h ol ders ( 4 8). T his is o ne of t he Pri mar y 
O bjecti ves of t his resear c h st u d y t hat t he Nati o nal I nstit utes of H ealt h has d ee me d 
i m p orta nt t o f u n d. 
 
P H Y SI C A L RI S K S  
 
Di s c o mf ort a n d di str e s s  
Ris k: Sali va sa m ples will be o btai ne d fr o m i nfa nts a n d c hil dre n b y use of a 
s p o n ge t hat will be s wa b be d al o n g t he c h ee ks a n d g u ms. T he de gree of dis c o mf ort 
is e x pecte d t o be mi ni mal b ut, as i n a n y ne w b or n w h o is dist ur be d, c o ul d ca use 
cr yi n g. T his sa m pli n g pr oce d ure was c h os e n f or t his st u d y t o mi ni mize i nfa nt 
disc o mf ort (c o m par e d t o ve ni p u nct ure or h eel- stic ks). We e x p ect t hat relati ves 
w h o are s a m ple d will t olerate t his pr oce d ure well.  
 
Miti g ati o n : We will o btai n t he s peci me ns as q uic kl y as p ossi ble (esti mate 5 - 1 0 
mi n utes) b y a n urse wit h e xte nsi ve e x perie nce ha n dli n g ne w b or n i nfa nts. If t he 
ne w b or n cries e xcessi vel y d uri n g t he pr ocess of sa m ple c ollecti o n t he c oll ecti o n 
will be st o p pe d. If i ns uffi cie nt sa m ple (e. g. o nl y o ne) has bee n o btai ne d t he n 
sa m ples fr o m t his i nfa nt will n ot be i ncl u de d i n t he st u d y. 
 
Effective ness: Hi g hl y eff ecti ve 
 
C o m pli c ati o n s of m e di c al m a n a g e m e nt  
 

 
Ris k: I nf a nts a n d c hil dre n i n t he st u d y ma y recei v e “ p ositi ve” ge n etic fi n di n gs 
t hat i n dicate a nee d f or m e dical i nter ve nti o n (l o n git u di nal care, s cree ni n g tests, 
pr oce d ur es). I n rar e cas es, s uc h f oll o w- u p ma y lea d t o u n necessar y i nter ve nti o ns 
i n t he case of false p ositi ves, or c o m plicati o ns of i nter ve nti o ns i n b ot h false 
p ositi ves a n d tr ue p ositi ves. 
Partici pa nts i n t he " Dia g n ose d" c o h ort will all be recei vi n g o n g oi n g sta n dar d 
cli nical car e i n t heir r es pecti ve cli nics, a n d t he g e netic res ults are n ot e x pecte d t o 
creat e a n y a d diti o nal ris k. We e x p ect t hat < 3 % of partici pa nts wil l ha ve pre vi o usl y 
u n k n o w n fi n di n gs fr o m t he N G S- N B S scree n or t he o pti o nal a d diti o nal cat e g ories 
of ge n o mic i nf or mati o n ( A me n d ola et al. 2 0 1 5). 
 
Miti g ati o n: A n y c hil dre n i n t he st u d y f o u n d t o ha ve a d diti o nal fi n di n gs will be 
referre d f or sta n dar d of care cli nical ma na ge m e nt. 
 
A d here n ce t o strict a n d c o nser vati ve defi niti o ns of “ pat h o ge nic” a n d “li kel y 
pat h o ge nic” v aria nt classificati o ns, a n d o verall r ules f or re p orti n g “ p ositi ve” 
fi n di n gs (as descri b e d i n 2) will ma xi mize s pecificit y a n d re d uce t h e c ha n ce o f 
false p ositi ve res ults. 
 
False p ositi ves will als o be mi ni mize d i n s o me c o n diti o ns i n w hic h c o nfir mat or y 
cli nical testi n g is a vaila ble (e g. bi oc h e mical assa ys or e nz y me  testi n g). 
 
All partici pa nts wit h p ositi ve N G S - N B S fi n di n gs will ha ve a sta n dar d- of-care 
cli nical f oll o w- u p pla n esta blis he d a n d will be referre d t o t he a p pr o priate 
s pecialists f or s ur veilla nce or treat me nt. 
 
Drs. C. P o well a n d B. P o well are b ot h pe di atricia ns as well as me dical g e neticists 
a n d ha ve e x perie n ce i n a p pr o priate me dical f oll o w- u p a n d referral t o s pecialists f or 
c hil dre n wit h ge netic dis or ders. 
 
Effective ness: M o der atel y effecti ve. O nce a p artici pa nt has e m bar k e d o n 
sta n dar d- of- care me di cal f oll o w - u p, we ca n n ot f urt her miti gate t he ris k of 
c o m plicati o ns t hat ma y occ ur. 
 
F ail ur e t o di a g n o s e 
Ris k: Beca use ne xt - g e nerati o n se q ue nci n g will n ot ac hie ve 1 0 0 % s e nsiti vit y, t here 
ma y be partici pa nts i n t h e st u d y wit h false ne gati v e res ults. I n a d diti o n, t he 
selecti o n of c o n diti o ns f or N G S-N B S will o nl y i ncl u de a s mall s u bset of all ge netic  
dis or ders. T h us, s o me partici pa nts ma y n ot be dia g n ose d wit h a c o n diti o n t hat is 
prese nt or will ma nifest i n t he f ut ure. T his is a n e xtre mel y u nli kel y o utc o me f or 
partici pa nts i n t he “ Dia g n ose d C o h ort” w h o ha v e k n o w n dia g n oses. I n a d diti o n, 
d ue t o t he ver y l o w pr e vale nce of ot her ge n etic c o n diti o ns, it is hi g hl y u nli kel y t hat 
a n y partici pa nts i n t he “ Well - C hil d c o h ort” will ha ve s uc h a c o n diti o n.  T his ris k is 
t heref or e e xtr e mel y l o w. 
 

 
Miti g ati o n: Partici pati n g i n t he N C N E X U S st u d y d oes n ot create a n y a d d iti o nal 
ris k of a misse d dia g n osis t ha n a n y ot her c hil d i n t he ge neral p o p ulati o n, si nce t he y 
will ha ve e q ui vale nt r o uti ne sta n dar d of care as w o ul d a n y ot her c hil d i n t he ge neral 
p o p ulati o n. I n a d diti o n, ele me nts of t he st u d y desi g n will miti gate a gai nst t his ris k: 
 
C o nti n ual i m pr o ve me nt of bi oi nf or matics pi peli nes a n d vari a nt 
i nter pretati o n pr oce d ures, wit h peri o dic rea nal ysis, will re d uce false 
ne gati ves b y e n ha n ci n g t he se nsiti vit y of t he N G S -N B S.  
 
P are nts will be offere d “i n dicati o n -base d rea n al ysis” i f s y m pt o ms 
de vel o p, t h us p ote ntiall y all o wi n g t he m t o arri ve at a dia g n osis faster 
t ha n if t he y wer e n ot partici pati n g i n t he st u d y. 
 
Effective ness: Hi g hl y eff ecti ve.  
S o ci al ri s k s 
C o nfi d e nti a lit y 
Ris k: L oss of c o nfi de ntialit y ( pers o nal healt h a n d ge netic i nf or mati o n) d u e t o 
i na d verte nt discl os ure of ge netic fi n di n gs c o ul d lea d t o a d vers e pers o n al 
ps yc h ol o gical ( m o der ate, rare) or fi na n cial i m pact (e. g. i na bilit y t o o btai n healt h or 
life i ns ura nce ( m o der ate, rare), or s ocial h ar m ( m o derate, rare). 
 
Miti g ati o n: We will a p pl y all reas o na bl e meas ures t o e ns ure c o nfi d e ntialit y f or 
researc h s u bjects. 
Si g ne d c o nse nt f or ms will be st ore d i n a l oc ke d office.  
Sa m ples (sali va, is olate d D N A, se q ue n ci n g li brar y sa m ples) a n d i n silic o 
data (r a w se q ue n ci n g dat a, ali g n me nt files, calle d varia nts) use d i n t his 
st u d y will be i de ntifie d usi n g a u ni q ue st u d y I D n u m ber. 
A pass w or d -pr otecte d s ec ure R E D Ca p d ata base ma na ge d b y N C Tra C S 
will c o ntai n t he li n k bet wee n t he patie nt i de ntit y a n d t he st u d y I D n u m b er, 
b ut t he researc h la b or at or y will n ot ha ve access t o patie nt i de ntifiers. 
S u bject i de ntif yi n g i nf or mati o n will be access e d o nl y b y st u d y pers o n nel 
wit h a “ nee d t o k n o w ” i d e ntif yi n g i nf or mati o n f or t he p ur p ose of 
i m ple me nti n g t he st u d y. 
I n t he cli nical la b orat or y, i de ntif yi n g i nfor mati o n will be pr otecte d i n t he 
sa me ma n ner as all ot her cli nical sa m ples mai ntai ne d t here. Fi nal ge n etic 
test re p orts ( w hic h d o i ncl u de t he partici pa nt's i de ntif yi n g i nf or mati o n) 
are ha n dl e d via t he U N C H os pitals M olec ular Dia g n ostic la b orat or y 
acc or di n g t o C LI A sta n d ar ds. Di gital c o pies of t h e fi nal re p orts will be 
pass w or d pr otecte d a n d p a per c o pi es will be st ore d i n l oc ke d ca bi nets i n 
a sec ur e offi ce  s pace. 
 
A n y ge netic test r es ults t hat are e ntere d i nt o t he electr o nic me dical rec or d  
after p are ntal c o nse nt will ha ve t he sa me HI P A A pr otecti o ns as a n y ot her 

 
me dical i nf or mati o n.  
 
Partici pa nts’ res p o nses t o q uesti o n naires will be e ntere d i nt o o ur sec ure 
data base a n d i de ntifie d o nl y b y t heir I D n u m ber. 
 
Sa m ples of relati ves will be la bele d usi n g a n assi g ne d  a n N C X n u m ber 
relate d t o t he c hil d's I D n u m ber (e. g. N C X _ 0 0 0 1 0- 1). T he sa m ples will be 
se nt t o t he M olec ular G e netics La b orat or y f or site-s pecific testi n g.  
 
F oll o wi n g testi n g, t he res ults will be c o n ve ye d t o t he ge netic 
c o u nsel or/ me dical g e neticist b y se c ure e mail a n d he or s he will c o m m u nicate 
t he res ults t o t he relati ve(s). T he c hil d's cli nical re p ort will be a me n de d a n d it 
will state if t here has b ee n a c ha n g e i n t he i nter pretati o n of t he res ults i n li g ht 
of t he a d diti o nal testi n g.   
 
Relati ves ma y be i de ntifi e d b y t heir rel ati o ns hi p t o t he c hil d (c hil d's pare nts) 
b ut n ot b y t heir na me or ot her i de ntif yi n g i nf or mati o n. Relati ves will n ot be 
iss ue d a n i n di vi d ual re p ort.  I n m ost cases, t he a d diti o nal testi n g will be of 
t he pare nts a n d t h e me dical ge neticist/ ge netic c o u nsel or will disc uss t he 
o pti o n of testi n g wit h t he m at t he ti me of t he ret ur n of t he c hil d's res ults.   
 
I n t he rar e case t hat a s a m ple fr o m relati ve w h o is n ot t he pare nt w o ul d be 
usef ul, t he ge netic c o u ns el or/ me dical ge n eticist will as k t h e pare nt t o c o ntact 
t he relati ve a n d h a ve t he relati ve c o ntact t he st u d y office t o sc h e d ule a st u d y 
visit at t he C T R C.  C o nse nt will be o btai ne d fr o m t he relati ve b y t he g e neti c 
c o u nsel or/ me dical g e neticist a n d t he sa m ple o btai ne d a n d pr ocesse d as 
descri be d a b o ve.  
 
Effective ness: Hi g hl y eff ecti ve 
 
Fi n a n ci al  
 
Ris k: T here is al wa ys a ris k t hat ge netic fi n di n gs c o ul d res ult i n fi na ncial ris k s uc h 
as l oss of i ns ura nce or e m pl o y me nt, h o we ver t hat ris k is ver y l o w, b ot h i n ge neral 
a n d i n t he c urr e nt st u d y. S o me p artici pa nts will recei ve ge n etic test res ults t hat ma y 
dia g n ose a partic ular c o n diti o n or i n dicate t hat t he partici pa nt is at-ris k t o d e vel o p a 
c o n diti o n i n t he f ut ure. 
 
F or partici pa nts i n t he “ Dia g n ose d c o h ort,” t h e ris ks are n ot greater t h a n 
t he y w o ul d be if t he partici pa nt were ha vi n g cli nical testi n g. T he ris k is 
s o me w hat greater i n s u m beca use m ore ge n es are bei n g a nal yze d a n d 
beca use of t he s mall c ha nce of a n a d diti o nal ge n o mic fi n di n g wit h 
si g nifica nt cli nical i m plicati o ns. 
 
F or partici pa nts i n t he “ Well-C hil d” c o h ort t here is a ver y s mall c ha n ce 

 
( < 3 %) of a fi n di n g i n t he cate g or y of “ N G S- N B S” res ults. H o we ver, si nce 
t hese fi n di n gs will be clearl y acti o na ble fr o m a m e dical sta n d p oi nt, t here 
w o ul d be a si g nifica nt m e dical be n efit t o t he s u bject a n y ti me s uc h a fi n di n g 
is re veale d. 
 
F or partici pa nts ra n d o mi ze d t o t he “ d ecisi o n gr o u p” of t he st u d y, t he 
ris ks of discl osi n g i nf or mati o n a b o ut a d diti o nal ge n o mic fi n di n gs are n ot 
k n o w n. 
 
Miti g ati o n: Fe der al le gislati o n calle d t he Ge n etic I nf or mati o n N o n discri mi nati o n 
Act ( GI N A) pr o hi bits t he use of ge netic i nf or mati o n t o discri mi nate a gai nst 
i n di vi d uals i n e m pl o y me nt a n d healt h i ns ura nce s etti n gs. T he i nf or me d c o nse nt 
pr ocess, as w ell as, t he c o nse nt f or ms (see N C N E X U S _c o nse nt _ p hase 
II _ dia g n ose d c o h ort: A p pe n di x 1 6 a n d N C N E X U S _c o nse nt _ p hase II _ Well- C hil d 
c o h ort: A p pe n di x 1 7) will i ncl u de a disc ussi o n of t he be nefits a n d t h e li mitati o ns of 
GI N A. T here are als o N ort h Car oli na state la ws t o pr otect a gai nst ge n etic 
discri mi nati o n. A maj or pr o visi o n of T he Aff or da ble Care A ct ( A C A) of 2 0 1 0 
pr o hi bits iss uers of healt h i ns ura nce fr o m discri mi nati n g a gai nst patie nts wit h 
ge netic diseas es b y ref usi n g c o vera g e beca use of ' pre -e xisti n g c o n diti o ns'. 
Pare nts will be i nf or me d t hat c urre nt la ws t hat pr otect a gai nst ge netic 
discri mi nati o n d o n ot a p pl y t o life i ns ura nce, disa bilit y i ns ura nce or l o n g- t er m care 
i ns ura nce ( N C N E X U S _ c o nse nt _ p hase II _ dia g n ose d c o h ort: A p pe n di x 1 6 a n d N C 
N E X U S _c o nse nt _ p has e II _ Well - C hil d c o h ort: A p pe n di x 1 7). E xte nsi ve ge netic 
c o u nseli n g will be pr o vi de d t o pare nts re gar di n g t h eir si g nifica nce of a n y fi n di n gs 
a n d rec o m me n d e d cli nical f oll o w- u p. Cli nicall y seri o us a d ult- o nset ge n o mic 
fi n di n gs f or w hic h t her e are n o a v aila ble treat me nts or pre ve nti ve strat e gies (f or 
e xa m ple, earl y o nset de m e ntia) will n ot be ret ur n e d t o pare nts. 
 
Effective ness: U ncertai n. GI N A d oes n ot pr ot ect s o me “ o pti o nal” f or ms of 
i ns ura nce, s uc h as disa bilit y, life or l o n g-ter m care i ns ura nce, s o t here is t he 
p ote ntial t hat partici pati o n i n t his st u d y c o ul d affect partici pa nts’ f ut ure i ns ura bilit y 
f or t hese i ns ur a nce t y pes. I n a d diti o n, t he la w d oes n ot a p pl y t o t he U. S. militar y. 
Li ke GI N A, t he A C A d o es n ot a p pl y t o n o n- healt h i ns ura nce t y pes. 
 
Gr o u p H ar m  
Ris k: Beca use w e ar e i ncl u di n g et h nic mi n orities t here is a c ha nce t hat s o me 
ge netic fi n di n gs mi g ht be re p orte d as li n ke d t o a p artic ular racial or et h nic gr o u p, 
pr o d uci n g w hat has b ee n descri be d as “ gr o u p h ar m.”  T he li keli h o o d of t his is 
esti mate d t o be rar e.  
 
Miti g ati o n: We, as cli nicia ns a n d researc hers, are se nsiti ve t o t his iss ue 
a n d will e n dea v or t o a v oi d s uc h iss ues w he n re p orti n g ge netic fi n di n gs of 
t he st u d y. 
 
Effective ness: Hi g hl y eff ecti ve 
 

 
F a mil y D y n a mi c s  
Ris k: As wit h a n y ge netic i nf or mati o n, t here is a p ossi ble ris k t hat fa mil y 
me m bers ma y res p o n d n e gati vel y t o ge netic i nf or mati o n t hat was lear n e d d uri n g 
t he c o urse of t h e res ear c h pr oject. T his is tr ue of a n y ge netic testi n g ( b ot h cli nical 
a n d researc h).  
 
Miti g ati o n: Pr ofessi o nal ge netic c o u nseli n g will b e pr o vi de d as p art of t he 
i nf or me d c o nse nt a n d ret ur n of res ults. 
 
Effective ness: M o der atel y effecti ve  
 
P s y c h ol o gi c al  ri s k s 
 
P are nt al e m oti o n al stress d ue t o st u d y p artici p ati o n 
Ris k: T here is a sli g ht ris k of pare nts e x perie n ci n g u nc o mf orta ble e m oti o nal states 
b y c o m pleti n g t he ps yc h os ocial assess me nts t hat as k s o me pers o nal q u esti o ns 
a b o ut q ualit y of life a n d e x perie n ces of recei vi n g dia g n ostic res ults or i nci de ntal 
fi n di n gs. T he de gree of t his ris k is esti mate d t o be rare t o i nfre q ue nt. 
 
Miti g ati o n: Beca use st u d y i nter vie ws a n d q uesti o n naires were c h os e n t o reflect 
w ha t are li kel y t o be pree xisti n g c o ncer ns, t he st u d y assess me nts are n ot e x pecte d 
t o mar ke dl y i ncrease partici pa nts’ ps yc h ol o gical distress. T he pr oject tea m als o 
has ha d e xte nsi ve e x peri e nce i n c o n d u cti n g assess me nts wit h i n di vi d uals a n d 
fa milies w h o recei ve ge n etic testi n g a n d fi n di n gs fr o m t h ose tests. Bef ore 
be gi n ni n g t he assess me nts a n d i nter vie ws, s u bjects will be re mi n de d t hat t he y ca n 
st o p t he i nter vie w at a n y ti me, or c h o ose n ot t o a ns wer s pecific q uesti o ns. 
 
Effective ness: Hi g hl y eff ecti ve 
 
P ar e nt al  di str e s s or a n xi et y r e g ar di n g p o siti v e g e n o mi c fi n di n g s  
Ris k: T he c hief ris k t o pare nts partici pati n g i n t his st u d y is a n xiet y or distress 
fr o m ha vi n g lear n e d of g e n o mic i nf or mati o n a b o ut t heir c hil d t hat pre dicts 
disease ris k or r e veals a pre dis p ositi o n t o a dis or der f or w hic h t here is n o 
c urre ntl y effecti ve i nter v e nti o n. F or pare nts of partici pa nts i n t he “ Dia g n os e d 
c o h ort,” t he ris k of a n y a d diti o nal distress or a n xiet y as a res ult of st u d y 
partici pati o n is mi ni mal. Pare ntal distress or a n xi et y is m ore li kel y w he n 
u ne x pecte d g e n o mic fi n di n gs are ret ur ne d. 
 
It is p ossi ble t hat fa mil y me m bers ma y res p o n d n e gati vel y t o ge netic 
i nf or mati o n t hat was lear ne d d uri n g t he c o urs e of t he researc h pr oject. T his is 
tr ue of a n y g e netic testi n g ( b ot h cli nical a n d researc h) a n d we e x p ect t hat 
pr ofessi o nal ge n etic c o u nseli n g pr o vi de d as part of t he ret ur n of res ults will 
miti gate t he ris k of s uc h o utc o mes. 
 

 
Dia g n ostic Fi n di n gs: T he ret ur n of res ults relate d t o a k n o w n dia g n osis is 
strai g htf or war d a n d n o n- c o ntr o versial. E moti o nal distress is p ossi ble a n y ti me 
t hat pare nts lear n t heir c hil d has a ge netic c o n diti o n.  H o we ver, pare nts 
partici pati n g i n t he “ Dia g n ose d c o h ort” alrea d y k n o w t hat t heir c hil d has a 
dis or der wit h a li kel y ge n etic eti ol o g y, a n d res earc h i n dicates t hat ris k is 
mi ni mal w he n ge netic i nf or mati o n is rela ye d b y a ge netic c o u nseli n g tea m i n a n 
a p pr o priate s etti n g. 
 
N G S - N B S Fi n di n gs: F or pare nts of partici pa nts wit h p ositi ve N G S-N B S  fi n di n gs 
( n ot relate d t o a k n o w n dia g n osis), t here is ris k f or a n a d vers e ps yc h ol o gical 
i m pact. We e x p ect t hat t he de gree of a n xiet y a n d distress w o ul d be e q ui val e nt t o 
t hat of pare nts w h os e c hil d recei ves a p ositi ve sta n dar d ne w b or n scree n res ult. 
T his ps yc h ol o gical reacti o n is li kel y t o be te m pere d b y t he me dicall y acti o n a ble 
nat u re of t he fi n di n gs. 
 
A d diti o nal ge n o mic fi n di n gs: F or pare nts ra n d o mi ze d t o t he “ d ecisi o n gr o u p” 
w h o c h o ose t o lear n a b o ut carrier stat us i n t heir c hil d, we e x pect t hat t he 
ps yc h ol o gical i m pact will be mi ni mal, a n d si milar t o t hat of pare nts w h o lear n 
t hat t heir c hil d is a carrier of C ystic Fi br osis or Sic kle Cell a ne mia t hr o u g h t he 
sta n dar d ne w b or n scr ee ni n g pr o gra m. F or t h ose w h o c h o ose t o lear n a d diti o nal 
dia g n ostic i nf or mati o n a b o ut t heir c hil d a n d s u bse q ue ntl y recei ve u ne x p ecte d 
i nf or mati o n i n dicati n g t heir c hil d has a g e netic healt h ris k, t he ma g nit u de of 
ps yc h ol o gical distress is u n pre dicta ble a n d de pe n ds o n t he pare nt a n d t h e 
fi n di n gs.  H o we ver, t h e c ha nce of s u c h fi n di n gs is ver y s mall. 
 
Miti g ati o n: T he ris ks ass ociate d wit h pare ntal res p o nses t o ge netic i nf or m ati o n 
a b o ut t heir c hil d ar e c o m ple x a n d f or m t he b asis of t he nee d f or t his researc h 
pr oject. We will pr o vi de ge netic c o u nseli n g a n d referral t o s pecialists as nee de d 
f or a n y p ositi ve res ults. 
 
All st u d y tea m me m bers w h o ha ve c o nt act wit h st u d y partici pa nts are alrea d y 
trai ne d ( p h ysicia ns a n d g e netic c o u nsel ors) t o rec o g nize a n d pr o b e i n dicat ors of 
p ossi ble distress (e. g., partici pa nts’ descri pti o n or dis pla y of distress- relat e d 
s y m pt o ms). 
 
We will c ollect data o n distress ( de pressi ve s y m pt o ms, a n xiet y) bef ore ret ur n  of 
res ults (t o esta blis h baseli ne le vels) a n d after ret ur n of res ults, all o wi n g us t o 
e xa mi ne c h a n ges i n distress o ver  ti me. 
T he decisi o n ai d is bei n g desi g ne d t o hel p 
fa milies u n dersta n d t he ris ks a n d be nefits of st u d y partici pati o n a n d ma ke a n 
i nf or me d c h oice base d o n t heir val ues a n d prefere nces.  
 
Pare nts are als o a ble t o c ha n ge t heir mi n ds a b o ut a n y c h oices ma d e as p art of t he 
st u d y bef ore i nf or mati o n is ret ur ne d t o t he m. 
 
Effective ness: M o der atel y effecti ve  

 
 
P ar e nt al d e ci si o n r e g r et 
Ris k: Pare nts i n t he st u d y ma y e x perie n ce re gret a b o ut t he decisi o n t he y ma ke wit h 
re gar d t o h a vi n g t heir c hil d se q ue nce d, or t heir c h oices t o recei ve or n ot t o recei v e 
certai n cate g ories of a d diti o nal ge n o mic i nf or mati o n. O ur e x perie nce i n t he cli nica l 
setti n g i n dicates t hat e m oti o nal distress re q uiri n g referrals is rare or i nfre q u e nt.  
O ur e x perie nce i n t he cli nical setti n g i n dicates t hat e m oti o nal distress re q uiri n g 
referrals is rare or i nfre q ue nt. I n a n earlier st u d y ( 1 8) t here w ere n o si g nifi ca nt 
d iffere n ces b et wee n 1 8 m ot hers of scree n-p ositi ve i nfa nts wit h Fra gile X 
pre m utati o n a n d 1 8 c o m paris o n m ot hers o n meas ures of a n xiet y, d e pressi o n, stress, 
or q ualit y of life. A s u bset of m ot hers e x peri e nce d cli nicall y si g nifica nt a n xiet y a n d 
decisi o n re gr et , b ut fact ors ass ociate d wit h t hese o utc o mes c o ul d n ot be i de ntifie d. 
Greater s p o usal s u p p ort was ge nerall y ass ociat e d wit h m ore p ositi ve o utc o mes. 
 
Miti g ati o n: Decisi o n re gret will be meas ure d aft er ret ur n of res ults. Sc ores will be 
a nal yze d t o d etect cli nicall y mea ni n gf ul i ncreas es ( 0. 5 sta n dar d d e viati o ns or m ore, 
acc or di n g t o r esearc h o n cli nicall y mea ni n gf ul c ha n ges a n d c ha n ges t hat are 
n oticea ble t o res ear c h partici pa nts).  
 
T he decisi o n ai d s h o ul d mi ni mize re gret b y e n a bli n g i nf or me d c h oices b as e d o n 
t he pare nts’ v al ues a n d prefere nces.  
 
A n y partici pa nts fla g g e d base d o n t hese m o nit ori n g met h o ds will be disc usse d wit h 
t he st u d y tea m, w hic h i ncl u des cli nical ge n eticists, certifie d g e netic c o u ns el ors, a n d 
ps yc h ol o gical resear c hers wit h e x pertise i n ps yc h ol o gical distress.  
 
F or a n y p are nts w h o d o e x perie nce distress, res earc h s u g gests it w o ul d li kel y 
i n v ol ve a n xiet y a n d decisi o n re gret rat her t ha n d e pressi ve s y m pt o ms or p o or 
q ualit y of life, s u g gesti n g t hat a d diti o nal c o u nseli n g w o ul d be a first-li ne res p o nse 
t o res ol ve t he distress, ps yc h ol o gical c o u nseli n g or si milar referrals ma y b e 
i n dicate d. 
 
Effective ness: Hi g hl y eff ecti ve 
 
P s y c h ol o gi c al i m p a ct o n c hil d/i nf a nt p arti ci p a nt s  
Ris k: Ret ur n of u ne x pect e d res ults i n t he c o nte xt of testi n g a mi n or raises ne w a n d 
c halle n gi n g iss ues re g ar di n g t he pr otecti o n of h u m a n s u bjects. T hese are m ostl y 
t he oretical ris ks, wit h o ut a great d eal of e m piric data t o i n dicate t he ma g nit u de or 
li keli h o o d of t hese ris ks. As s uc h, o ne of t he k e y g oals of t he N C N E X U S pr oject 
is t o be gi n t o pr o vi de e vi de nce o n t he ps y c h ol o gical i m pact of ge netic t esti n g i n 
c hil dre n. T he m ost c o m m o n t y pe of “ u ne x pecte d ” res ult ( u nrelate d t o a 
partici pa nt’s dia g n osis) i n t his st u d y will be carrier stat us f or a recessi ve dis or der, 
w hic h we e x p ect t o ha v e a ver y l o w c h a nce of ha vi n g a detri me ntal ps yc h ol o gical 
i m pact. Ot her p ote ntiall y m ore c o ncer ni n g fi n di n gs t hat w o ul d i n dicate t he li kel y 
f ut ure o nset of disease will be m uc h less li kel y, esti mate d at < 3 % of t h e c o h ort.  

 
P ossi ble ps yc h ol o gical ris ks i ncl u de: 
 
V ul nera ble c hil d s y n dr o me i n w hic h ge netic fi n di n gs e xacer bate c hil d h o o d 
de vel o p me ntal or a dj ust me nt pr o ble ms 
 
A ba n d o n me nt or ne glect of t he c hil d as a res ult of ge netic fi n di n gs 
 
A br o gati o n of t he f ut ur e “ri g ht n ot t o k n o w” ge netic i nf or mati o n 
 
Mit i g ati o n: T he N C N E X U S st u d y f oll o ws t he m o del of i nf or me d, s hare d 
decisi o n ma ki n g b y pr o vi di n g e d ucati o nal res o urces ( u n dersta n d a ble decisi o n ai ds 
paire d wit h c o u nseli n g) t o hel p e ns ure, usi n g ri g or o us practices, t hat p are nts are 
a de q uatel y pr e pare d f or t his i nf or mati o n. If s u c h iss ues arise as a res ult of l ear ni n g 
a n u ne x pecte d ge n o mic fi n di n g, we ha ve e xt e nsi ve l ocal e x p erie nce a n d res o urces 
t o hel p i n s uc h sit uati o ns. 
 
Dr. C. P o well r u ns a pre-s y m pt o matic H u nti n gt o n disease testi n g pr o gra m a n d has 
e x peri e n ce i n s uc h sit uati o ns. Dr. Ber g, Dr. B. P o well a n d Ms. R oc he ha v e ha d 
e xte nsi ve e x perie nce ret ur ni n g dia g n ostic, me dicall y acti o na ble a n d a d diti o nal 
fi n di n gs i n b ot h a cli nical a n d researc h setti n g. 
 
Fa milies e x perie nci n g si g nifica nt distress as a res ult  of u ne x pecte d fi n di n gs will 
be ref err e d t o a p pr o priate me ntal healt h s pecialists as nee de d. Si nce cli nical 
ge neticists a n d certifie d ge netic c o u nsel ors will be o n t he tea m c o n v e yi n g t hese 
res ults, o ur e x perie nce i n t he cli nical setti n g i n dicates t hat s uc h e m oti o nal distress 
re q uiri n g referrals is rar e. 
 
Pare nts will n ot be a ble t o re q uest res ults t hat w o ul d i n dicate a ris k of a n a d ult- 
o nset c o n diti o n f or w hic h t here is n o c urre nt treat me nt, s uc h as A L S.  
 
Effective ness: U ncertai n. S o me p ote ntial har ms, s uc h as t he l o n g- ter m i m plicati o ns 
of lear ni n g a b o ut g e n o mic i nf or mati o n i n a healt h y ne w b or n, are u n k n o w n a n d 
s o me w hat u n pre dict a ble, a n d ma y ma nifest l o n g after c o m pleti o n of t he st u d y. 
Alt h o u g h we pla n t o f oll o w partici pa nts l o n git u di nall y as l o n g as p ossi ble, we 
ca n n ot g uar a ntee t hat f u n di n g will e xist f or l o n g-ter m u ni nterr u pte d m o nit ori n g of 
o utc o mes deca d es fr o m n o w.  
 
7.  A D V E R S E E V E N T  R E C O R DI N G/ R E P O R TI N G  
T he st u d y tea m has c o nsi dera ble e x pertise i n c o n d ucti n g assess me nts wit h 
i n di vi d uals a n d fa milies w h o recei ve ge n etic testi n g a n d fi n di n gs fr o m t h ose tests. 
Ke y pers o n n el i n t his gra nt i ncl u de certifie d g e netic c o u nsel ors, cli nical 
ge neticists, me dical bi oc he mical ge neticists a n d a ne ur ol o gist, all of w h o m ha ve 
e xte nsi ve e x perie nce wit h me dical ma na ge m e nt o f rare ge netic c o n diti o ns a n d 
deali n g wit h patie nt res p o nses t o ge netic i nf or mati o n i ncl u di n g ne w b or n scree ni n g 
res ults i n a cli nical setti n g. 

 
 
• 
A d v er s e E v e nt  D efi niti o n s  
T he N C N E X U S st u d y itself d oes n ot raise s u bsta ntial ris ks f or a n y of t he 
f oll o wi n g a dverse e ve nts:  
• 
Seri o us i nj ur y or ill ness 
• 
H os pitalizati o n  
• 
Disa bilit y  
• 
Life -t hreate ni n g a d verse effect  
 
8.  M e di c al m a n a g e m e nt of k n o w n  di a g n o s e s:  
Partici pa nts i n t he “ Dia g n ose d C o h ort” will ha ve o n g oi n g me dical care f or t heir 
k n o w n c o n diti o ns, s o me of w hic h i ncl u de t he p ote ntial f or seri o us ill nesses, 
h os pitalizati o ns, or e ve n deat h. H o we v er, e nr oll me nt i n t he N C N E X U S researc h 
pr oject will n ot c o nstit ute a n y i ncrease d ris k f or s uc h c o m plicati o ns, w het her or 
n ot a m olec ular dia g n osis is o btai ne d.  Partici pa nts i n t he “ Well- C hil d C o h ort” 
will li ke wise ha ve t he p ote ntial t o de vel o p a n y t y pical i nj ur y or pe diatric ill ness. 
A gai n, e nr oll me nt i n t he N C N E X U S researc h pr oject will n ot c o nstit ute a n y 
i ncreas e d ris k f or t hes e c o m m o n c o n diti o ns. T heref ore, we will n ot c o nsider 
i nterc urr e nt ill nesses, s p ora dic i nj uries, or t he w orse ni n g of e xisti n g c o n diti o ns as 
a d verse e ve nts ass o ciate d wit h t he st u d y.  
 
• 
M e di c al m a n a g e m e nt of n e wl y i d e ntifi e d  di a g n o s e s:  
P ositi ve fi n di n gs fr o m t he N C N E X U S st u d y ma y lea d t o cli nical f oll o w - u p a n d 
p ossi bl y me dical i nter ve nti o ns as part of t he cli ni cal ma na g e me nt of a n e wl y 
dia g n ose d ge netic c o n diti o n. T hese o utc o mes are e x pecte d a n d will be d oc u me nte d 
as part of t he l o n git u di nal f oll o w- u p of partici pa nts wit h p ositi ve fi n di n gs. 
T heref ore, w e wil l n ot c o nsi der t he e xiste nce of a d diti o nal treat me nt or f urt her 
dia g n ostic tests as a n a d v erse e v e nt. H o we v er, t here ma y be i nsta n ces i n w hic h 
p h ysicia ns ta ke acti o ns d ue t o a ge netic fi n di n g, b ut t hese acti o ns are n ot 
c o nsi dere d t o be sta n d ar d of care.  I n a d diti o n, t here ma y be rare i nsta n ces i n w hic h 
t he sta n dar d of car e ma n a ge me nt of a di a g n ose d g e netic c o n diti o n lea ds t o 
c o m plicati o ns t hat w o ul d ne gati vel y i m pact t he cli nical utilit y of t he ge netic res ult.  
T heref ore, w e will m o nit or f or a n y s u c h a d verse e ve nts, defi ne d as:  
 
• 
A d v er s e eff e ct s a s s o ci at e d wit h t h e i n v e sti g ati o n al d e vi c e 
d u e t o  m e di c al i nt er v e nti o n s u n d ert a k e n a s a 
r e s ult of p o siti v e fi n di n g s: 
1.  T here is a reas o n a ble p ossi bilit y t hat err o ne o us ( n o n-sta n dar d of 
care) me dical acti o ns ma y ha ve occ urre d as a c o nse q ue nce of 
p ositi ve fi n di n gs. 
2.  T here is a reas o n a ble p ossi bilit y t hat seri o us i nj ur y, 
h os pitalizati o n, or deat h ma y ha ve occ urre d as a c o m plicati o n of 
sta n dar d of care me dical f oll o w - u p of p ositi ve fi n di n gs. 
 

 
d ue  t o f alse p ositi ve fi n di n gs: T here is a reas o na ble 
p ossi bilit y t hat me dical acti o ns ta ke n b y t he patie nt’s 
p h ysicia n were relat e d t o a ge netic fi n di n g t hat w as later 
dee me d t o be a false p ositi ve  res ult. 
 
• Ot h er u n e x p e ct e d a d v er s e  eff e ct s:  
T he N C N E X U S st u d y  ma y als o i n v ol ve ris k f or u ne x pecte d a d vers e effects, 
w hic h we defi ne as a n y i nci de nt, e x peri e nce, or o utc o me t hat meets all of t he 
f oll o wi n g criteria: 
• 
U ne x pect e d i n nat ure, se verit y, or fre q ue n c y (i.e. n ot descri be d i n st u d y -
relate d d o c u me nts s uc h as t he I R B-a p pr o v e d pr ot o c ol or c o ns e nt f or m, t he 
i n vesti gat ors br oc h ure, et c.)  
• 
Relate d or p ossi bl y relate d t o partici pati o n i n t he researc h (i. e. p ossi bl y 
relate d  mea ns  t here  is  a  reas o na ble  p ossi bilit y  t hat  t he  i nci de nt  
e x perie n ce,  or  o utc o m e  ma y  ha v e  b ee n  ca u s e d  b y  t he  pr oce d ures  
i n v ol ve d i n t he researc h) 
• 
S u g gests t hat t he researc h places s u bjects or ot h ers at greater ris k 
of har m (i ncl u di n g p h ysi cal, ps yc h ol o gical, ec o n o mic, or s ocial 
har m).  
 
R e c or di n g a n d A s s e s s m e nt of A d v er s e  Eff e ct s  
All o bser ve d or v ol u nteere d a d verse effects, re g ar dless of c o h ort or ra n d o mizati o n 
gr o u p, t hat ha ve a reas o na ble p ossi bilit y of a ca us al relati o ns hi p t o t he 
i n vesti gati o nal de vice will be rec or d e d i n t he R E D Ca p data bas e e ntr y f or t he 
partici pa nt.  F or all a d verse effects, s uffic i e nt i nf or mati o n will be p urs ue d a n d/ or 
o btai ne d s o as t o per mit 1) a n a de q u ate det er mi nati o n of t he o utc o me of t h e effect 
(i.e., w het her t he effect s h o ul d be classifie d as a seri o us a d vers e effect) a n d; 2) a n 
assess me nt of t he ca usal relati o ns hi p bet wee n t h e a d verse effect a n d t h e 
i n vesti gati o nal de vice or, if a p plica ble, t he ot her s u bse q ue nt treat me nt or di a g n ostic 
pr oce d ur e. 
 
T he mi ni m u m i nitial i nf or mati o n t o be ca pt ure d i n t he s u bject’s 
R E D Ca p f or m c o ncer ni n g t he a d vers e de vice effect i ncl u des: 
•  A narr a ti ve descri pti o n of t he e ve nt  
•  Classificati o n of t he e ve nt’s se verit y a n d rati o nale f or  classificati o n  
•  I n v esti gat or assess me nt of t he ass ociati o n bet w ee n t he e ve nt a n d st u d y 
treat me nt 
•  C urre nt  stat us 
R e p orti n g a d v er s e eff e ct s t o  F D A  
 
• A d verse De vice Effects  
T he N C N E X U S st u d y itself d oes n ot raise s u bsta ntial ris ks f or a n y of t he 

 
f oll o wi n g a d verse d e vice e ve nts: 
 
 Res ults i n  deat h  
 Is life-t hreate ni n g 
 Res ults i n per ma ne nt i m pair me nt of a b o d y f u n cti o n or per ma n e nt 
da ma ge  t o b o d y str uct ure 
 Necessitates me di cal or  s ur gical i nter ve nti o n t o precl u de per ma ne nt 
i m pair me nt of a b o d y f u n cti o n or per ma n e nt da ma ge t o a b o d y str uct ure 
• -or - 
 A pre vi o us a d verse e v e nt t hat was n ot i nitiall y dee me d re p orta bl e b ut is 
later f o u n d t o fit t he criteria f or re p orti n g n ote d a b o ve (re p orti n g s uc h 
e ve nts wit hi n 1 0 w or ki n g da ys fr o m w he n e ve nt w as dee me d re p orta ble).  
S uc h re p orts will be s u b mitte d wit hi n 1 0 
w or ki n g d ays U n a ntici p ate d A dverse D evice Effects 
( U A D Es) 
T he N C N E X U S d oes n ot c o nte m plate ha vi n g U A D Es ass ociate d wit h t his st u d y. 
 
• Wit h dr a w al of I R B a p pr o v al  
T he S p o ns or s hall n otif y t he F D A, all partici pati n g I R Bs a n d partici pati n g 
i n vesti gat ors of a n y wit h dra wal of a p pr o val of t he st u d y b y a re vie wi n g I R B 
wit hi n 5 w or ki n g d ays after recei pt of t he wit h dra wal of a p pr o v al. 
 
• F D A Re p ort i n g Pr ocess 
 
Me dical D e vice Re p orts, w het her f or a ntici p ate d or u na ntici pate d de vice -relate d 
effects, ar e t o be s u b mitte d o n F D A F or m 3 5 0 0 A. T he c o ntact i nf or mati o n f or 
s u b mitti n g M D R re p orts is n ote d bel o w: 
 
F o o d a n d Dr u g A d mi nistrati o n 
Ce nter f or D e vices  a n d Ra di ol o gical Healt h 
Me dical De vice Re p orti n g  
P O B o x 3 0 0 2 
R oc k ville, M D  2 0 8 4 7- 3 0 0 3 
 
R e p orti n g a d v er s e eff e ct s t o t h e r e s p o n si bl e  I R B 
Fe deral r e g ulati o ns re q uire ti mel y re p orti n g b y i n vesti gat ors t o t heir l ocal I R B 
of u na ntici pate d pr o bl e ms p osi n g ris ks t o s u bjects or ot hers. T he f oll o wi n g 
descri bes t he U N C - C H I R B re p orti n g re q uire me nts, t h o u g h I n vesti gat ors at 
partici pati n g sites are res p o nsi ble f or meeti n g t he s pecific re q uire me nts of t heir 
I R B of r ec or d. 

 
 
• R e p ort Pr o m ptl y, b ut n o l at er t h a n 5 w or ki n g d a y s:  
Researc h ers are r e q uire d t o s u b mit re p orts of t he f oll o wi n g pr o ble ms pr o m ptl y 
b ut n o later t ha n 1 0 w or ki n g da ys fr o m t he ti me t he i n vesti gat or bec o m es a ware 
of t he e ve nt: 
 U n a ntici p ate d pr o ble ms i ncl u di n g a dverse eve nts t h at are 
u ne x pecte d a n d rel ate d  
o  U nex pecte d : A n eve nt is “ u nex pecte d ” w he n its s pecificity a n d severity are 
n ot acc ur ately reflecte d i n t he pr ot oc ol-rel ate d d o c u me nts, s uc h as t he 
I R B- a p pr ove d rese arc h pr ot oc ol, a ny a p plic a ble i nvesti g at or br oc h ure, 
a n d t he c urre nt I R B- a p pr ove d i nf or me d c o ns e nt d oc u me nt a n d ot her 
relev a nt s o urces of i nf or m ati o n, s uc h as pr o d uct l a beli n g a n d p ack a ge 
i nserts. 
o  Rel ate d t o t he rese arc h pr oce d ures : A n eve nt is rel ate d t o t he rese arc h 
pr oce d ures if i n t he o pi ni o n of t he pri nci p al i nvesti g at or or s p o ns or, t he 
eve nt w as m ore likel y t h a n n ot t o be c a use d by t he rese arc h pr o ce d ures.  
o  H ar mf ul : eit her c a use d h ar m t o s u bjects or ot hers, or pl ace d t he m at 
i ncre ase d risk 
 
 U n a ntici p ate d a dverse device effect : A n y seri o us a d verse effect o n healt h 
or safet y or a n y life- t hreateni n g pr o ble m or deat h ca use d b y, or ass ociate d 
wit h, a de vice, if t hat effect, pr o ble m, or d eat h was n ot pre vi o usl y 
i de ntifie d i n nat ure, se v erit y, or de gree of i nci de nce i n t he i n vesti gati o nal 
pla n or a p plicati o n (i ncl u di n g a s u p ple me ntar y pla n or a p plicati o n, or a n y 
ot her u na ntici pate d s eri o us pr o ble m ass ociate d wit h a de vice t hat relates t o 
t he ri g hts, safet y, or w elfare of s u bjects. 
 
• Ot h er R e p ort a bl e e v e nt s:  
T he f oll o wi n g e ve nts als o re q uire pr o m pt re p orti n g t o t he I R B, t h o u g h n o later 
t ha n 1 0 w or ki n g da ys: 
 
•  
C o m pl ai nt of a rese arc h s u bject w he n t he c o m plai nt i n dicates u ne x pecte d 
ris ks, or t he c o m plai nt ca n n ot be res ol ve d b y t he researc h tea m. 
•  
Pr ot oc ol devi ati o ns or vi ol ati o ns (i ncl u des i nte nti o nal a n d 
acci de nt al/ u ni nte nti o nal de viati o ns fr o m t he I R B a p pr o ve d pr ot o c ol) f or 
a n y of t he f oll o wi n g sit uati o ns: 
o  o ne or m ore p artici p a nts were pl ace d at i ncre as e d risk of h ar m 
o  t he eve nt h as t he p ote nti al t o occ ur a g ai n 
o  t he devi ati o n w as necess ary t o pr otect a s u bject fr o m i m me di ate h ar m 
•  Bre ac h of  c o nfi de nti alit y 
 
Re p orti n g Pr ocess  

 
T he re p ort a ble e v e nts n ote d a b o ve will be re p orte d t o t he I R B usi n g t he f or m: 
“ Re p orta ble E v e nt F or m ” or as a writte n re p ort of t he e ve nt (i ncl u di n g a 
descri pti o n of t he e v e nt wit h i nf or mati o n re gar di n g its f ulfill me nt of t he a b o ve 
criteria, f oll o w- u p/res ol uti o n a n d nee d f or re visi o n t o c o nse nt f or m a n d/ or ot her 
st u d y d oc u me ntati o n). 
 
C o pies of eac h re p ort a n d d oc u me ntati o n of I R B n otificati o n a n d recei pt will be 
ke pt i n t he Cli nical I n vesti gat or’s st u d y file.  
 
Wit h dr a w al of s u bj e ct s fr o m t h e  st u d y  
T he i nf or me d c o ns e nt materials will clearl y state t hat pare nts ca n wit h dra w fr o m 
t he st u d y at a n y ti me, t hat t his will n ot i m pact t he c hil d's me dical care i n a n y wa y. 
Pare nts w h o ref use t o use t he decisi o n ai ds or fail t o c o m pl y wit h t he 
q uesti o n n aires will be c o nsi dere d wit h dra w n a n d t heir c hil d’s sa m ple will n ot 
u n der g o f urt h er se q u e nci n g or a nal ysis. T he y will n ot partici pate i n t he 
ra n d o mizati o n. S peci me ns fr o m pare nts w h o d esire t o ter mi nate partici p ati o n will 
be destr o ye d a n d n o f urt h er a nal ysis of d ata i n s uc h i n di vi d uals will be p urs ue d. 
 
Descri pti o n of I nvesti g ati o n al  Device  
O n A u g ust 2 7, 2 0 1 4, t he F D A pr o vi d e d a res p o nse t o a pre-s u b missi o n i n q uir y a n d 
deter mi ne d t hat t he pr o p ose d N C N E X U S st u d y w o ul d be re q uire d t o s u b mit a n 
I n v esti gati o nal De vice E xe m pti o n (I D E) d ue t o t h e si g nifica nt ris k ass ociat e d wit h 
t he p ote ntial l o n g-ter m c o nse q ue nces t o b ot h t he pare nt(s) (i.e., ps yc h ol o gical 
i m pact) a n d t he c hil d (i.e., de nial of life a n d/ or l o n g- disa bilit y i ns ura nce a n d ha vi n g 
me dical rec or ds c o ntai ni n g W E S i nf or mati o n of w hic h he/s he di d n ot c o nse nt t o) 
after lear ni n g of t he W E S fi n di n g. T he F D A has deter mi ne d t hat t he decisi o n ai d 
t hat will be de vel o pe d a n d t he ps yc h os ocial res earc h t hat will be c o n d ucte d are als o 
part of t he “ d e vice” t hat is b ei n g e val uate d.  I n t hat case, t he “ d e vice” w o ul d be 
best descri be d  as:  
 
“I nf or me d p ar e ntal decisi o n - ma ki n g ai de d b y a n electr o nic decisi o n ai d 
re gar di n g t heir acce pta n ce of ne xt- g e nerati o n se q u e nci n g ne w b or n scree ni n g 
f or t heir c hil d; w h ole e x o me se q ue nci n g wit h tar g ete d a nal ysis a n d Sa n g er 
c o nfir mati o n of p ositi ve fi n di n gs; ret ur n of res ults t hr o u g h sta n dar d- of -care 
ge netic c o u nseli n g; a n d f oll o w- u p q uesti o n naires re gar di n g t he ps yc h os o cial 
i m pact of t he scr ee ni n g.” 
 
T his de vice e n c o m passes all as pects of  o ur st u d y, i ncl u di n g i nf or me d c o nse nt 
f or ms, s hare d- decisi o n m a ki n g t o ols (i.e., electr o ni c decisi o n ai d), sa m ple 
c ollecti o n, ne xt- ge n erati o n se q ue nci n g, bi oi nf or matics pi peli nes i ncl u di n g varia nt 
calli n g a n d selecti o n al g orit h ms, c o nfir mati o n of varia nts wit h Sa n ger se q u e nci n g, 
pr oce d ur es f or ret ur ni n g differe nt cate g ories of ge n o mic res ults t o pare nts, a n d 
f oll o w- u p pr oce d ures wit h pare nts bef ore a n d after lear ni n g of researc h res ults 
( q uesti o n naires). 
 

 
Eac h of t he ste ps i n v ol ve d i n t he N C N E X U S pr oject ca n b e e n visi o ne d as a n 
ele me nt of a n i nstr ucti o n al ma n ual c o ntai ni n g ( b ut n ot li mite d t o) t he f oll o wi n g 
i nstr ucti o ns of use: scri pt use d f or t he i nitial recr uit me nt, st u d y br oc h ure, decisi o n 
ai ds, q uesti o n naires, c o ns e nt f or ms, sa m ple c ollecti o n, la b orat or y met h o ds ( D N A 
e xtracti o n, e x o me li br ar y pre parati o n, a n d massi vel y parallel se q ue n ci n g), 
bi oi nf or matics pi peli ne (i nitial i nf or matics a nal ysis a n d varia nt a n n ot ati o n), cli nical 
i nter pretati o n of e x o m e s e q ue nce varia nts (s cree ni n g a n d i n dicati o n-base d 
a nal ysis), varia nt c o nfir mati o n b y Sa n ger se q ue n ci n g (i n t he C LI A-certifi e d 
M olec ular G e netics La b orat or y), ra n d o mizati o n, ret ur n of res ults, a n d ot her 
detaile d pr oce d ures d escri bi n g preca uti o ns a n d safe g uar ds t hat will be utilize d 
bef ore a n d aft er t he p are nt s ha ve bee n i nf or me d of t he i n vesti gati o nal res ults. T h us, 
t he “ de vice” is all as pects of t he st u d y as descri b e d a b o ve. 
 
P ossi ble m o dificati o ns t o t he de vice t hat w e ca n a ntici pate occ urri n g t hr o u g h o ut t he 
st u d y are disc usse d i n pr e vi o us secti o ns a n d briefl y s u m marize d here. T he cli nical 
acti o na bilit y of all Me n delia n dis or ders will c o nti n ue t o e v ol ve o ver t h e f oreseea ble 
f ut ure. T he d e vel o p me nt of t he list of c o n diti o ns t hat ha ve bee n sc ore d b y t he N C 
N E X U S Acti o na bilit y tea m ( A p pe n di x 8) as descri be d i n S ecti o n 2, Defi ni n g 
Cli nical Acti o na bilit y is e x pecte d t o c o nti n ue t hr o u g h o ut t he st u d y peri o d a n d after, 
a n d t heref ore, p eri o dic u p dates of t he lists will occ ur. Sli g ht c ha n ges or a dj ust me nts 
base d o n fee d bac k fr o m user testi n g ma y lea d t o mi n or c ha n ges i n t he L o n git u di nal 
St u d y Meas ures ( A p p e n di x 1 9) descri be d i n Secti o n 5, St u d y Narrati ve. A m o n g t he 
maj or researc h acti vities of t he N C N E X U S pr oject will be t he e val uati o n of ne w 
bi oi nf or matics al g orit h ms; i n a d diti o n, we a ntici pate i m pr o ve me nt i n t he e vi de nce 
a vaila ble t o assess p at h o ge nicit y of varia nts (as d efi ne d i n Secti o n 2 Re vise d 
Res ults i n t he  F oll o w- u p Pr oce d ures, Secti o n). T h us, b y desi g n t here will be 
de vel o p me ntal c h a n ges i n t he pr ot oc ol, acc o m pa nie d b y peri o dic rea nal ysis of t he 
N G S data, wit h  t he p ossi bilit y t hat t he res ults of t he a nal ysis ma y c h a n ge o ver ti me 
a n d s o me partici pa nts will be re- c o nt acte d f or u p date d res ults. T his sit uati o n will 
be clearl y descri b e d i n t he i nf or me d c o ns e nt. 
 
T he F D A will be pr o vi de d wit h a 5- da y n otice of a n y u p dates or c h a n ges i n t he 
meas ures, lists t hat are i m ple me nte d i n t he i nf or matics al g orit h ms, or t y pes of 
re vise d res ults t hat are r et ur ne d t o patie nts.  
 
M o nit ori n g Pl a n/ Pr oce d ures 
T he S p o ns or-i n vesti gat or ( Pri nci pal I n vesti gat or) a n d ke y st u d y pers o n n el wi ll meet 
o n a q uarterl y basis t o disc uss as pects of t he st u d y, re vie w u na ntici p ate d pr o ble ms 
a n d a d vers e e v e nts, e val u ate res ults, scr uti nize d at a a n d a ntici pate pr o ble ms 
rele va nt t o s u bject safet y. A n i n de pe n de nt St u d y D ata M o nit or a n d Me dical Safet y 
M o nit or will be esta blis he d pri or t o e nr oll me nt of partici pa nts. T hese i n di vi d uals 
will meet wit h t he Pri nci pal I n v esti gat or a n d ot her ke y st u d y pers o n nel as descri be d 
bel o w. 
 
As o ur st u d y i n v ol ves a u ni q ue as pect of g e n o mic se q ue nci n g i n t he pe diatric 
p o p ulati o n n ot t y picall y c o nsi dere d u n d er m ost “ me dical m o nit ori n g” pla ns, 

 
i ncl u di n g t he o pti o n f or s o me pare nts t o recei ve res ults o n varia nts i n ge nes t hat are 
ass ociate d wit h carrier stat us a n d a d ult - o nset c o n diti o ns i n t heir i nfa nt, we hel d a 2-
da y c o nfere n ce at t he b e gi n ni n g of o ur pr oject t o s olicit o pi ni o ns a b o ut o ur 
pr o p ose d st u d y pr ot oc ol i ncl u di n g ret ur n of res ults fr o m a n e xter nal gr o u p of 
c o ns ulta nts i ncl u di n g e x perts i n bi o me dical et hics, ge netic c o u nseli n g, ne w b or n 
scree ni n g a n d cli nical ge netics. We recei ve d s u p p ort f or o ur pla n as o utli ne d a b o ve. 
T hese e x p erts ha ve a gree d t o c o nti n ue t o ser ve as e xter nal c o ns ulta nts t hr o u g h o ut 
o ur st u d y peri o d a n d i ncl u de Dr. Eric J u e n gst, Direct or of t he U N C Ce nter f or 
Bi oet hics, as well as ot hers fr o m o utsi de o ur i nstit uti o n. T he y will be a vaila ble as 
nee de d t o r e vie w a n y et hical c o ncer ns or q uesti o ns t hat arise.  
 
S T U D Y D A T A  M O NI T O R  
T he data i n t his st u d y will be re vie w e d o n a re g ular basis b y a n i n de pe n d e nt data 
m o nit or. T he r ole of t he data m o nit or will be t o re vie w st u d y d oc u me ntati o n, 
re g ulat or y files, a n d i nf or me d c o nse nt t o e ns ure t h e q ualit y a n d i nte grit y of t he data 
c ollecte d a n d a d her e nce t o g o o d cli nical practices. A n i m p orta nt f oc us of t h e data 
m o nit ori n g will be t o e ns ure a p pr o priate i nf or m e d c o nse nt has bee n o btai ne d fr o m 
t he researc h partici pa nts.  
 
M E DI C A L S A F E T Y  M O NI T O RI N G  
T he Pri nci pal I n vesti gat or will o versee t he s afet y of t he st u d y at her site. T his 
safet y m o nit ori n g will i ncl u de caref ul assess me nt a n d a p pr o pri ate re p orti n g of 
a d verse e ve nts as n ote d a b o ve. Me dical m o nit ori n g will i ncl u de a re g ular 
assess me nt of t he n u m ber a n d t y pe of a d vers e e ve nts as defi ne d i n secti o n 8. A n y 
safet y c o n cer ns or u na ntici pate d pr o ble ms will be rela ye d t o a n i n d e pe n de nt 
me dical saf et y m o nit or f or i m me diate re vie w. I n a d diti o n, t here will be a q uarterl y 
pr oject meeti n g at w hic h c o ncer ns ca n b e raise d f or disc ussi o n b y t he e ntire pr oject 
tea m. S uc h o p p ort u nities will all o w us t o m o nit or f or t he e x pecte d ps yc h os o cial 
i m pact of ge netic testi n g as well as bei n g al ert t o ot her wise u ne x p ecte d p artici pa nt 
safet y iss ues. T he me di cal safet y m o nit or will ha ve e x pertise i n p e diatrics a n d 
researc h et hics. T h e r ole of t he me dical officer will be t o a d vise t he Pri nci p al 
I n v esti gat or a n d pr oj ect t ea m a n d ma k e rec o m me n dati o ns a b o ut c o nti n ui n g t he 
st u d y. 
 
A U DI TI N G A N D  I N S P E C TI N G 
T he i n vesti gat or will per mit st u d y -relate d m o nit ori n g, a u dits, a n d i ns pecti o ns 
b y t he E C/I R B, t he s p o ns or, g o ver n me nt re g ulat or y b o dies, a n d U ni versit y 
c o m plia nce a n d q u alit y ass ura nce gr o u ps of all st u d y- relate d d o c u me nts a n d 
st u d y-relate d files. T h e i n vesti gat or will hel p c o or di nate i ns pecti o ns of 
a p plica ble st u d y- r elate d f acilities. 
Partici pati o n as a n i n vesti gat or i n t his st u d y i m plies acce pta nce of p ote ntial 
i ns pecti o n b y g o ver n me nt re g ulat or y a ut h orities a n d a p plica ble U ni versit y 
c o m plia nce a n d q u alit y ass ura nce offices.  
 
A D DI TI O N A L R E C O R D S A N D  R E P O R T S  
Re p orts fr o m t he st u d y data m o nit or descri bi n g rec or ds re vie we d, a n y c o ncer ns 

 
n ote d, a n d rec o m me n dati o ns ma de t o c orrect deficie ncies; as well as 
c orres p o n d e nce fr o m t he me dical safet y m o nit or f oll o wi n g a n y necessar y 
re vie ws will be pr o vi de d t o t he I R B, F D A, a n d N H G RI/ NI C H D. Re p orti n g will 
als o i ncl u de a n n ual pr o gr ess re p orts t o N H G RI/ NI C H D. 
 
D A T A H A N D LI N G A N D R E C O R D  K E E PI N G  
M ost of t he data c ollect e d i n t he N C N E X U S st u d y will be st ore d 
electr o nicall y as f oll o ws (a n d detaile d b el o w):  
•  A R E D Ca p data bas e ma na ge d b y t he N ort h Car oli na Tra nslati o nal a n d 
Cli nical Scie nces ( N C Tra C S) I nstit ute will be use d t o st ore de m o gra p hic 
i nf or mati o n a n d baseli ne cli nical data f or eac h partici pa nt ( pare nts a n d 
c hil dre n) e nr olle d i n t he cli nical st u d y. T his data base is wit hi n t he U N C 
H os pitals fire wall a n d will ser ve as t he dat a base of rec or d li n ki n g 
pers o nall y i de ntifia ble i nf or mati o n wit h t he u ni q ue st u d y i de ntifier. E ntr y 
a n d mai nte na nce of t he st u d y rec or ds will be a s hare d res p o nsi bilit y of 
st u d y i n vesti gat ors. 
•  Pr oject -relat e d tas ks a n d la b orat or y dat a will be rec or de d i n a c ust o m 
w or kfl o w ma na g e me nt s yste m ma na ge d b y R E N CI t hat has access 
restricte d t o s pecific r oles. N o pers o nall y i de ntifia ble healt h i nf or mati o n 
is i ncl u de d. 
•  Data fr o m q u esti o n naires will be st ore d o n a sec ure dri ve at U N C wit h 
restricte d access t o o nl y t h ose pers o n nel w h o are i n v ol ve d i n data 
a nal ysis. 
•  Data fr o m t he d ecisi o n ai d will be st ore d o n a sec ure dri ve at R TI wit h 
restricte d access t o o nl y t h ose pers o n nel w h o are i n v ol ve d i n data 
a nal ysis. 
•  Se q ue nce d ata a n d calle d varia nts will be st ore d i n t he U N C Researc h 
C o m p uti n g s yste m. Ra w se q ue nce d ata will be st ore d f or t he d urati o n of t h e 
st u d y o n ta pe bac k u p t hr o u g h U N C Researc h C o m p uti n g. A re d uce d 
re pres e ntati o n of t he partici pa nt’s varia nt calls (c urre ntl y i n t he f or m of a 
V C F file, alt h o u g h sta n d ar d f or mats ma y c ha n g e o ver ti me) a n d a file t hat 
c o m prises t he cli nicall y rele va nt vari a nts t o be re vie we d a n d c o nfir me d will 
be st ore d i n a dat a re p osit or y ma na g e d b y R E N CI a n d will ha ve access 
restricte d t o a s u bset of st u d y pers o n nel w h o are i n v ol ve d i n data a n al ysis. 
 
Res ults t hat are c o nfir m e d i n t he M G L will be re p orte d as cli nical g e netic t est 
res ults a n d par e nts will be pr o vi de d wit h a pa p er c o p y of t he re p ort f or t heir 
pers o nal rec or ds. T h ese official re p orts will ha ve p artici pa nt na mes a n d me dical 
rec or d n u m b ers a n d, if c o nse nt is gi ve n, will bec o me part of t he p er ma ne nt me dical 
rec or d, s u bject t o t he pr otecti o ns aff or d e d b y t he HI P A A re g ulati o ns. Ot her wise, 
s u bject na mes or ot her directl y i de ntifia ble i nf or m ati o n will n ot a p pear o n a n y 
re p orts, p u blicati o ns, or ot her discl os ures of cli nical st u d y o utc o mes. 
 
R e c or d M ai nt e n a n c e a n d  R et e nti o n  
T he i n vesti gat or-s p o ns or will mai ntai n rec or ds i n acc or da n ce wit h G o o d Cli nical 
Practice g ui deli nes, t o i n cl u de:  

 
 
 F D A c orres p o n d e nce rel ate d t o t he I D E a p plicati o n a n d I n vesti gati o nal Pla n  
o  I R B c orres p o n de n ce relat e d t o t he cli nical pr ot oc ol, c urre nt a n d 
past versi o ns of t he I R B-a p pr o ve d cli nical pr ot oc ol a n d 
c orres p o n di n g I R B -a p pr o ve d c o nse nt f or ms 
 Si g ne d I n v esti gat or’s A gree me nts a n d Certificati o ns of Fi na nci al 
I nterests of Cli nical I n vesti gat ors 
 Certificates of re q uire d trai ni n g (e. g., h u ma n s u bject pr otecti o ns, G o o d 
Cli ni cal Practice, etc.) f or i n vesti gat or -s p o ns or a n d liste d s u b-
i n vesti gat ors 
 Si g ne d i nf or me d c o nse nt f or ms 
 C o pies of a d vers e e ve nt re p orts a n d a n n u al or i nteri m re p orts 
 M o nit ori n g visit re p orts 
 Fi nal cli nical st u d y  re p ort. 
C o nfi d e nti alit y  
I nf or mati o n a b o ut st u d y s u bjects will be ke pt c o nfi de ntial a n d ma na ge d acc or di n g 
t o t he re q uire me nts of t h e Healt h I ns ura nce P orta bilit y a n d Acc o u nta bilit y Act of 
1 9 9 6 ( HI P A A). T h os e re g ulati o ns re q uire a si g ne d s u bject a ut h orizati o n i nf or mi n g 
t he s u bject of t he f oll o wi n g: 
 W h at pr otect e d healt h i nf or mati o n ( P HI) will be c ollecte d fr o m s u bjects 
i n t his st u d y 
 W h o will ha ve access t o t hat i nf or mati o n a n d w h y  
 W h o will use or discl ose t hat i nf or mati o n 
 T he ri g hts of a r esearc h s u bject t o re v o ke t heir a ut h orizati o n f or use of t heir 
P HI.  
 
I n t he e ve nt t hat a s u bj ect re v o kes a ut h orizati o n t o c ollect or use P HI, t he 
i n vesti gat or, b y re g ulati o n, retai ns t he a bilit y t o use all i nf or mati o n c ollecte d pri or 
t o t he re v ocati o n of s u bject a ut h orizati o n. F or s u bjects t hat ha ve re v o ke d 
a ut h orizati o n t o c ollect or use P HI, atte m pts s h o ul d be ma de t o o btai n per missi o n 
t o c ollect at least vital stat us (i.e. t hat t he s u bject is ali ve) at t he e n d of t heir 
sc he d ule d st u d y peri o d. 
 
All cli nical i nf or mati o n will be ke pt c o nfi de ntial, a n d will o nl y be acces se d b y 
t h ose directl y i n v ol ve d i n t he researc h. T h e F D A ma y re q uest a n d b e gra nt e d 
access t o t he rec or ds. T h e di gital file c o ntai ni n g t he li n ke d partici pa nt na m es, U N C 
me dical rec or d n u m bers a n d u ni q ue st u d y i de ntifiers will be st ore d i n a p ass w or d-
pr otecte d R E D Ca p d ata b ase ma na g e d b y N C Tra C S. Pa per c o pies of c o ns e nt f or ms 
a n d a n y pers o n al healt h i nf or mati o n will be st ore d i n a l oc ke d fili n g ca bi net i n a 
l oc ke d office. All i de ntifiers ( na me, d ate of birt h, etc.) will be re m o ve d fr o m t he 
sali va sa m ples bef or e t he y are se nt t o t he B S P or M G L a n d all sa m ples use d i n t his 
st u d y will be la bele d o nl y wit h t he partici pa nt’s u ni q ue st u d y i de ntifier. 
 
Ge netic varia nt data: Eac h partici pa nt’s ge n etic varia nt data will be st ore d usi n g a 
u ni q ue partici pa nt I D n u m ber a n d st ore d f or t he d urati o n of t he st u d y o n ta pe 

 
bac k u p t hr o u g h U N C Researc h C o m p uti n g. A file t hat c o m prises t he cli nicall y 
rele va nt varia nts t o be r e vie we d a n d c o nfir me d will be st ore d i n a data re p osit or y 
ma na ge d b y R E N CI, w hi c h will ha ve access restri cte d t o a s u bset of st u d y 
pers o n nel. A r e d uce d re prese ntati o n of t he p artici pa nt’s varia nt calls will be st ore d 
wit h t he u ni q ue partici pa nt I D n u m b er t o all o w f or re- a nal ysis. 
 
Q uesti o n naire Res p o nses: Partici pa nts’ res p o nses t o st u d y q uesti o n naires (researc h 
data) will be i de ntifie d o nl y b y t heir u ni q ue partici pa nt I D n u m ber, w h et her 
c ollecte d i n a n o nli ne q u esti o n naire f or m at i m ple me nte d i n Q ualtrics or i n a pa per-
a n d- pe ncil q uesti o n nair e or i nter vie w b y a trai ne d staff me m ber (e. g., f or 
partici pa nts w h o ca n n ot or prefer n ot t o c o m plete t he o nli ne q uesti o n naire). T he 
q uesti o n naires will n ot c ollect i nf or mati o n t hat c o ul d be use d t o i de ntif y 
partici pa nts.  
 
Decisi o n Ai d Usa ge Data: Data gat here d t hr o u g h p artici pa nt i nteracti o n wit h t he 
electr o nic d ecisi o n ai d ( e. g., a p p perf or ma nce metrics, usa ge metri cs, a n d 
partici pa nt i n p uts) will be ass ociate d wit h u ni q ue partici pa nt I D n u m bers. T he 
decisi o n ai d will n ot c ollect i nf or mati o n t hat c o ul d be use d t o i de ntif y 
partici pa nts. All usa ge data will be st ore d i n a sec ur e pass w or d pr otect e d data base 
at R TI s ec ur e d b y i n d ustr y sta n dar d fire walls a n d a stri n ge nt I T sec urit y p olic y 
fra me w or k. Data a n d q uer y t o ols p u blis he d via we b i nterfaces will be e ncr y pte d.