TITLE: TMA-TNP  Design
AUTHORS: Heidi Feiler, Koei Chin

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Human Tumor Atlas Tissue MicroArrary TNP  (TMA-TNP)</div><br/><div class = "text-block">The Tissue MicroArray (TMA) TNP will extend the  SARDANA-TNP characterization and analytics methodologies for evaluation and validation on a large array of breast tumor samples that provide a broad spectrum of disease state and subtype. A commercially available anonymized breast tumor TMA was purchased and sections distributed to participating HTAN Centers. Some deidentified basic clinical data will also be provided. The participating HTAN Centers will characterize the FFPE specimens (e.g. by imaging) and generate a spatially resolved cell type/state census using each Center’s method of choice. Data will then be recorded in a common repository to enable joint analysis.</div><br/><div class = "text-block">This TNP has two specific Aims focused on (i) Data Collection and (ii) Data Coordination and Analysis. Individual Centers can participate in one or both aims.</div><br/><div class = "text-block">This protocol outlines the design of the TMAs and provides the basic clinical sample descriptions.</div></div>

[STEPS]
?. [TMA Map of Participant IDs]
A custom breast TMA design generated by Dr. Koei Chin (OHSU) was sent to Pantomics for  TMA FFPE block generation and sectioning.  The randomized array design, outlined below, was used to generate 2 identical TMAs, TMA1 and TMA2.  Cores from tumor samples with Pantomics Ref. No. were arrayed as shown (the matching HTAN Participant IDs are also shown).  ABC1Array PositionPantomics Ref. No.HTAN Participant ID2A01F11-0369HTA14_13A02F08-3884HTA14_24A03F11-0957HTA14_35A04F08-0824HTA14_46A05F18-0992HTA14_57A06255287-OHSUHTA14_68A07F13-1953HTA14_79A08F11-3564HTA14_810A09316473-OHSUHTA14_911A10F10-1047HTA14_1012A11MCF10A-KCHTA14_1113B01F16-0582HTA14_1214B02HCC1143HTA14_1315B03F08-1273HTA14_1416B04F17-3395A3HTA14_1517B05F10-0051HTA14_1618B06F10-0992HTA14_1719B07F09-1280HTA14_1820B08HCC3153HTA14_1921B09F16-0582HTA14_1222B10F09-0328HTA14_2023B11MDAMB436-KCHTA14_2124C01F09-3051HTA14_2225C02F13-0368HTA14_2326C03F10-0572HTA14_2427C04F09-1290HTA14_2528C05F11-3564HTA14_829C06316473-OHSUHTA14_930C07F09-4287HTA14_2631C08F10-0572HTA14_2432C09F10-4365HTA14_2733C10F08-1426HTA14_2834C11HCC1143-KCHTA14_2935D01255287-OHSUHTA14_636D02F16-2497HTA14_3037D03F09-2873HTA14_3138D04F10-0587HTA14_3239D05T47DHTA14_3340D06F09-0328HTA14_2041D07F09-1814HTA14_3442D08232527-OHSUHTA14_3543D09AU565HTA14_3644D10F08-3884HTA14_245D11HCC3153-KCHTA14_3746E01F15-0002HTA14_3847E02F08-0824HTA14_448E03326007-OHSUHTA14_3949E04F18-0992HTA14_550E05F10-1015HTA14_4051E06F11-0957HTA14_352E07F08-1273HTA14_1453E08F09-3051HTA14_2254E09F10-0587HTA14_3255E10F08-0773HTA14_4156E11AU565-KCHTA14_4257F01F10-4365HTA14_2758F02F09-4287HTA14_2659F03F13-1953HTA14_760F04F09-3432HTA14_4361F05F10-0342HTA14_4462F06F15-0002A1HTA14_3863F07F16-2497HTA14_3064F08F10-1047HTA14_1065F09F11-1210HTA14_4566F10F09-2873HTA14_3167F11BT474-KCHTA14_4668G01F10-1015HTA14_4069G02F09-1814HTA14_3470G03F11-1210HTA14_4571G04232527-OHSUHTA14_3572G05F11-0369HTA14_173G06F08-0773HTA14_4174G07F13-0368HTA14_2375G08326007-OHSUHTA14_3976G09F10-0992HTA14_1777G10F09-1290HTA14_2578G11T47D-KCHTA14_4779H01BT474HTA14_4880H02F09-3034HTA14_4981H03F09-1280HTA14_1882H04F08-1426HTA14_2883H05MDAMB436HTA14_5084H06F10-0051HTA14_1685H07F09-3432HTA14_4386H08F09-3034HTA14_4987H09F17-3395HTA14_1588H10F10-0342HTA14_4489H11MCF10AHTA14_51
ABC1Array PositionPantomics Ref. No.HTAN Participant ID2A01F11-0369HTA14_13A02F08-3884HTA14_24A03F11-0957HTA14_35A04F08-0824HTA14_46A05F18-0992HTA14_57A06255287-OHSUHTA14_68A07F13-1953HTA14_79A08F11-3564HTA14_810A09316473-OHSUHTA14_911A10F10-1047HTA14_1012A11MCF10A-KCHTA14_1113B01F16-0582HTA14_1214B02HCC1143HTA14_1315B03F08-1273HTA14_1416B04F17-3395A3HTA14_1517B05F10-0051HTA14_1618B06F10-0992HTA14_1719B07F09-1280HTA14_1820B08HCC3153HTA14_1921B09F16-0582HTA14_1222B10F09-0328HTA14_2023B11MDAMB436-KCHTA14_2124C01F09-3051HTA14_2225C02F13-0368HTA14_2326C03F10-0572HTA14_2427C04F09-1290HTA14_2528C05F11-3564HTA14_829C06316473-OHSUHTA14_930C07F09-4287HTA14_2631C08F10-0572HTA14_2432C09F10-4365HTA14_2733C10F08-1426HTA14_2834C11HCC1143-KCHTA14_2935D01255287-OHSUHTA14_636D02F16-2497HTA14_3037D03F09-2873HTA14_3138D04F10-0587HTA14_3239D05T47DHTA14_3340D06F09-0328HTA14_2041D07F09-1814HTA14_3442D08232527-OHSUHTA14_3543D09AU565HTA14_3644D10F08-3884HTA14_245D11HCC3153-KCHTA14_3746E01F15-0002HTA14_3847E02F08-0824HTA14_448E03326007-OHSUHTA14_3949E04F18-0992HTA14_550E05F10-1015HTA14_4051E06F11-0957HTA14_352E07F08-1273HTA14_1453E08F09-3051HTA14_2254E09F10-0587HTA14_3255E10F08-0773HTA14_4156E11AU565-KCHTA14_4257F01F10-4365HTA14_2758F02F09-4287HTA14_2659F03F13-1953HTA14_760F04F09-3432HTA14_4361F05F10-0342HTA14_4462F06F15-0002A1HTA14_3863F07F16-2497HTA14_3064F08F10-1047HTA14_1065F09F11-1210HTA14_4566F10F09-2873HTA14_3167F11BT474-KCHTA14_4668G01F10-1015HTA14_4069G02F09-1814HTA14_3470G03F11-1210HTA14_4571G04232527-OHSUHTA14_3572G05F11-0369HTA14_173G06F08-0773HTA14_4174G07F13-0368HTA14_2375G08326007-OHSUHTA14_3976G09F10-0992HTA14_1777G10F09-1290HTA14_2578G11T47D-KCHTA14_4779H01BT474HTA14_4880H02F09-3034HTA14_4981H03F09-1280HTA14_1882H04F08-1426HTA14_2883H05MDAMB436HTA14_5084H06F10-0051HTA14_1685H07F09-3432HTA14_4386H08F09-3034HTA14_4987H09F17-3395HTA14_1588H10F10-0342HTA14_4489H11MCF10AHTA14_51
?. [TMA Clinical Sample Descriptions]
ABCDEFGH1HTAN
 Participant IDAgeSexAnat.  SitePathologyGradeClinic stage
  (TNM)Subtybe2HTA14_2543FBreast&nbsp;Invasive ductal
  carcinoma&nbsp;IT2N2M0Luminal A3HTA14_3455FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N2M0Luminal A4HTA14_543FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0Luminal A5HTA14_1048FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IT1N1M0Luminal A6HTA14_156FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N2M0Luminal A7HTA14_1444FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N1M0Luminal B Her2+8HTA14_2837FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT4N0M0Luminal B Her2+9HTA14_2647FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N1M0Luminal B Her2+10HTA14_4469FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0Luminal B Her2+11HTA14_3249FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0Luminal B Her2+12HTA14_4137FBreastInvasive ductal carcinoma&nbsp;IIIT1N0M0Luminal B HER-13HTA14_443FBreastInvasive ductal
  carcinoma&nbsp;IIT1N0M0Luminal B HER-14HTA14_2459FBreastInvasive lobular
  carcinoma&nbsp;IIT2N0M0Luminal B HER-15HTA14_1743FBreastInvasive ductal
  carcinoma&nbsp;IIT2N0M0Luminal B HER-16HTA14_4069FBreastInvasive ductal
  carcinoma&nbsp;IIT2N1M0Luminal B HER-17HTA14_2065FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0Her2 over-expression18HTA14_1842FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIIT2N0M0Her2 over-expression19HTA14_3152FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IT2N2M0Her2 over-expression20HTA14_2250FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0Her2 over-expression21HTA14_4340FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIIT2N0M0Her2 over-expression22HTA14_2732FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIIT3N0M0TNBC23HTA14_376FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0TNBC24HTA14_4551FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIIT2N0M0TNBC25HTA14_839FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0TNBC26HTA14_2330FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIIT3N2M0TNBC27HTA14_4967FBreast&nbsp;Invasive lobular carcinoma&nbsp;IIT3N1M0Invasive lobular carcinoma&nbsp;28HTA14_1655FBreast&nbsp;Invasive lobular
  carcinoma&nbsp;IIT4N3M0Invasive lobular carcinoma&nbsp;29HTA14_742FBreast&nbsp;Invasive lobular
  carcinoma&nbsp;IIT2N3M0Invasive lobular carcinoma&nbsp;30HTA14_1238FBreast&nbsp;Invasive lobular
  carcinoma&nbsp;IIT2N0M0Invasive lobular carcinoma&nbsp;31HTA14_3049FBreast&nbsp;Invasive lobular
  carcinoma&nbsp;IT3N2M0Invasive lobular carcinoma&nbsp;32HTA14_385MTonsilNormal Tonsil  Normal Tonsil33HTA14_1568MJejunumNormal
  Jejunum  Normal
Jejunum34HTA14_13  Breast
  cell lineHCC1143  Basal Like35HTA14_19  Breast
  cell lineHCC3153  Basal Like36HTA14_33  Breast
  cell lineT47D  Luminal A37HTA14_48  Breast
  cell lineBT474  Luminal B38HTA14_36  Breast
  cell lineAU565  Her2 over-expression39HTA14_50  Breast
  cell lineMDAMB436  Claudin Low40HTA14_51  Breast
  cell lineMCF10A  Cystic fibrosis41HTA14_243FNormal BreastNormal Breast
  to IDC  NB-1A42HTA14_35  Normal
  BreastNormal
  Adacent Tissue  NB-2A43HTA14_6  Normal
  BreastNormal
  Adacent Tissue  NB-3A44HTA14_39  Normal
  BreastTrue
  Normal&nbsp;  NB-4A45HTA14_9  Normal
  BreastTrue
  Normal&nbsp;  NB-5B46HTA14_47Breast cell lineHCC1143  Luminal A47HTA14_46Breast cell lineHCC3153  Luminal B48HTA14_42Breast cell lineT47D  HER249HTA14_37 Breast cell lineBT474  Basal Like50HTA14_29 Breast cell lineAU565  Basal Like51HTA14_21 Breast cell lineMDAMB436  Claudin Low52HTA14_11 Breast cell lineMCF10A  Cystic fibrosis
ABCDEFGH1HTAN
 Participant IDAgeSexAnat.  SitePathologyGradeClinic stage
  (TNM)Subtybe2HTA14_2543FBreast&nbsp;Invasive ductal
  carcinoma&nbsp;IT2N2M0Luminal A3HTA14_3455FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N2M0Luminal A4HTA14_543FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0Luminal A5HTA14_1048FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IT1N1M0Luminal A6HTA14_156FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N2M0Luminal A7HTA14_1444FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N1M0Luminal B Her2+8HTA14_2837FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT4N0M0Luminal B Her2+9HTA14_2647FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N1M0Luminal B Her2+10HTA14_4469FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0Luminal B Her2+11HTA14_3249FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0Luminal B Her2+12HTA14_4137FBreastInvasive ductal carcinoma&nbsp;IIIT1N0M0Luminal B HER-13HTA14_443FBreastInvasive ductal
  carcinoma&nbsp;IIT1N0M0Luminal B HER-14HTA14_2459FBreastInvasive lobular
  carcinoma&nbsp;IIT2N0M0Luminal B HER-15HTA14_1743FBreastInvasive ductal
  carcinoma&nbsp;IIT2N0M0Luminal B HER-16HTA14_4069FBreastInvasive ductal
  carcinoma&nbsp;IIT2N1M0Luminal B HER-17HTA14_2065FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0Her2 over-expression18HTA14_1842FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIIT2N0M0Her2 over-expression19HTA14_3152FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IT2N2M0Her2 over-expression20HTA14_2250FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0Her2 over-expression21HTA14_4340FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIIT2N0M0Her2 over-expression22HTA14_2732FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIIT3N0M0TNBC23HTA14_376FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0TNBC24HTA14_4551FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIIT2N0M0TNBC25HTA14_839FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIT2N0M0TNBC26HTA14_2330FBreast&nbsp;Invasive
  ductal carcinoma&nbsp;IIIT3N2M0TNBC27HTA14_4967FBreast&nbsp;Invasive lobular carcinoma&nbsp;IIT3N1M0Invasive lobular carcinoma&nbsp;28HTA14_1655FBreast&nbsp;Invasive lobular
  carcinoma&nbsp;IIT4N3M0Invasive lobular carcinoma&nbsp;29HTA14_742FBreast&nbsp;Invasive lobular
  carcinoma&nbsp;IIT2N3M0Invasive lobular carcinoma&nbsp;30HTA14_1238FBreast&nbsp;Invasive lobular
  carcinoma&nbsp;IIT2N0M0Invasive lobular carcinoma&nbsp;31HTA14_3049FBreast&nbsp;Invasive lobular
  carcinoma&nbsp;IT3N2M0Invasive lobular carcinoma&nbsp;32HTA14_385MTonsilNormal Tonsil  Normal Tonsil33HTA14_1568MJejunumNormal
  Jejunum  Normal
Jejunum34HTA14_13  Breast
  cell lineHCC1143  Basal Like35HTA14_19  Breast
  cell lineHCC3153  Basal Like36HTA14_33  Breast
  cell lineT47D  Luminal A37HTA14_48  Breast
  cell lineBT474  Luminal B38HTA14_36  Breast
  cell lineAU565  Her2 over-expression39HTA14_50  Breast
  cell lineMDAMB436  Claudin Low40HTA14_51  Breast
  cell lineMCF10A  Cystic fibrosis41HTA14_243FNormal BreastNormal Breast
  to IDC  NB-1A42HTA14_35  Normal
  BreastNormal
  Adacent Tissue  NB-2A43HTA14_6  Normal
  BreastNormal
  Adacent Tissue  NB-3A44HTA14_39  Normal
  BreastTrue
  Normal&nbsp;  NB-4A45HTA14_9  Normal
  BreastTrue
  Normal&nbsp;  NB-5B46HTA14_47Breast cell lineHCC1143  Luminal A47HTA14_46Breast cell lineHCC3153  Luminal B48HTA14_42Breast cell lineT47D  HER249HTA14_37 Breast cell lineBT474  Basal Like50HTA14_29 Breast cell lineAU565  Basal Like51HTA14_21 Breast cell lineMDAMB436  Claudin Low52HTA14_11 Breast cell lineMCF10A  Cystic fibrosis