# Diagnosis of Fanconi Anemia: Mutation Analysis by Multiplex Ligation-Dependent Probe Amplification  and PCR-Based Sanger Sequencing

Authors: Johan J. P. Gille; Karijn Floor; Lianne Kerkhoven; Najim Ameziane; Hans Joenje; Johan P. de Winter
Journal: Anemia
 (2012)

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## Abstract

Fanconi anemia (FA) is a rare inherited disease characterized by developmental defects, short stature, bone marrow failure, and a high risk of malignancies. FA is heterogeneous: 15 genetic subtypes have been distinguished so far. A clinical diagnosis of FA needs to be confirmed by testing cells for sensitivity to cross-linking agents in a chromosomal breakage test. As a second step, DNA testing can be employed to elucidate the genetic subtype of the patient and to identify the familial mutations. This knowledge allows preimplantation genetic diagnosis (PGD) and enables prenatal DNA testing in future pregnancies. Although simultaneous testing of all FA genes by next generation sequencing will be possible in the near future, this technique will not be available immediately for all laboratories. In addition, in populations with strong founder mutations, a limited test using Sanger sequencing and MLPA will be a cost-effective alternative. We describe a strategy and optimized conditions for the screening ofFANCA, FANCB, FANCC, FANCE, FANCF, and FANCG and present the results obtained in a cohort of 54 patients referred to our diagnostic service since 2008. In addition, the follow up with respect to genetic counseling and carrier screening in the families is discussed.


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## Body

## 1. Introduction

Fanconi anemia (FA) is a rare inherited syndrome with diverse clinical symptoms including developmental defects, short stature, bone marrow failure, and a high risk of malignancies. Fifteen genetic subtypes have been distinguished: FA-A, -B, -C, -D1, -D2, -E, -F, -G, -I, -J, -L, -M, -N, -O, and -P. [1–4]. The majority of patients (~85%) belong to the subtypes A (~60%), C (~10–15%), or G (~10%), while a minority (~15%) is distributed over the remaining 12 subtypes, with relative prevalences between <1 and 5%. These percentages may differ considerably within certain ethnic groups, due to founder effects. All subtypes seem to fit within a “classical” FA phenotype, except for D1 and N (mutated in BRCA2/FANCD1and PALB2/FANCN), which are associated with a distinct, more severe, syndromic association. The mode of inheritance for all subtypes is autosomal recessive, except for FA-B, which is X-linked. These two different modes of inheritance have important consequences for the counseling of FA families. The relative prevalence of FA-B amongst unselected FA patients is estimated at 1.6% [5]. For all genetic subtypes disease genes have been identified (Table 1). Many mutations found in the various subtypes are private, but recurrent mutations are known, particularly in specific ethnic backgrounds (Table 2).Table 1
Fanconi anemia complementation groups, genes, and proteins.
GroupGene symbol(s)aCytogenetic locationProtein (amino acids)Domain structure (references)AFANCA16q24.31455HEAT repeats [8]BFANCBXp22.31859—CFANCC9q22.3558HEAT repeats [8]D1bBRCA213q12.33418RAD51- and DNA-binding motifs [9]D2FANCD23p25.31451—EFANCE6p21.3536—FFANCF11p15374—GFANCG9p13622Tetratricopeptide repeats (TPR) [10]IFANCI15q26.11328—JbBRIP117q221249DNA helicase [11, 12]LFANCL2p16.1375RING finger motif (E3 ligase) [7, 8]MFANCM14q21.32014DNA helicase, nuclease [13]NbPALB216p12.11186—ObRAD51C17q25.1376—PbSLX416p13.31834Endonuclease scaffold [3, 4]aFor gene nomenclature see http://www.genenames.org/.bThe proteins defective in groups D1, J, N, O, and P (boldface) act downstream or independent of the monoubiquitination of FANCD2; all other FA proteins act upstream of this process.Table 2
Major recurrent mutations in FA.
GeneMutation*Geographic/ethnic backgroundCommentReferencesFANCAc.3788_3790del (p.Phe1263del)European, BrazilianRelatively mild[14, 15]c.1115_1118delTTGG (p.Val372fs)EuropeanRelatively mild[16]Exon 12–17delExon 12–31delSouth-AfricanRelatively common in Afrikaners[17]c.295C>T (p.Gln99X)Spanish Gypsy populationWorldwide highest prevalence of mutantFANCA allele[18]FANCCc.711+4A>T (originally reported as IVS4+4A>T)Homozygous in 80% of Ashkenazi Jewish FA; relatively common in Japan.Severe phenotype in Jews, milder in Japanese.[19–22]c.67delG (originally reported as 322delG)Homozygous in approx. 50% of Dutch FA patientsLike other exon 1 mutations, relatively mild phenotype.[19, 23–25]FANCD2c.1948-16T>GTurkishFounder mutation[26]FANCGc.313G>T (p.Glu105X)European44% of mutatedFANCG alleles in Germany.[27]c.1077-2A>GPortuguese/BrazilianFounder mutation[27, 28]c.1480+1G>CFrench-CanadianFounder mutation[28]c.307+1G>CJapaneseFounder mutation[28, 29]c.1794_1803del (p.Trp599fs)European[28]c.637_643del (p.Tyr213fs)Sub-Saharan Africa82% of all black FA patients[30]FANCJc.2392C>T (p.Arg798X)Found in ca. 50% of FA-J patients of diverse ancestry; ancient mutation or hot spot.[11, 12]Nucleotide numbering based onATG = +1.Published sequence variations in FA genes, with their descriptions conforming to the current nomenclature rules, are listed athttp://www.rockefeller.edu/fanconi/.Most FA genes encode orphan proteins with no known molecular function. At least eight FA proteins (FANCA, -B, -C, -E, -F, -G, -L, and -M) assemble into a nuclear multiprotein core complex, which is required to activate FANCD2 and FANCI by monoubiquitination [6]. FANCL, which carries a RING finger domain, is supposed to represent the ubiquitin E3 ligase in this activation [7]. FANCM probably acts as a sensor of DNA damage and recruits the FA core complex to the site of damage, but FANCM also interacts with other proteins including Blm [6]. Monoubiquitination of FANCD2 and FANCI directs these proteins to areas of damaged chromatin where they interact with other proteins, resulting in repair of the damage [6]. The remaining FA proteins function downstream of or parallel to the FANCD2 activation step [6]. The exact nature of the DNA damage response, which when defective causes FA, remains to be defined. FANCJ/BRIP1 and FANCM possess DNA helicase motifs, which strongly suggests that the FA pathway acts through a direct interaction with DNA, presumably to resolve or remodel blocked DNA replication forks resulting from DNA interstrand cross-link damage [6]. This idea is strengthened by the recent extension of the FA pathway with SLX4, a scaffold protein for structure-specific endonucleases involved in unhooking the DNA cross-link [3, 4].


## 2. Laboratory Diagnostics in FA

Cells derived from FA patients are—by definition—hypersensitive to chromosomal breakage induced by DNA cross-linking agents such as mitomycin C (MMC) or diepoxybutane (DEB) [31]. This cellular phenotype is ascertained using stimulated blood T lymphocytes. The indications for FA laboratory testing are rather broad [32]. As a consequence, in only a small proportion of patients (about 10%) the chromosomal breakage test is positive, and an FA diagnosis is established. Since mutation testing by Sanger sequencing and MLPA is rather laborious, time consuming and therefore expensive, a positive chromosomal breakage test is a prerequisite for starting mutation screening. Confirmation of the FA diagnosis at the DNA level is important in patients in whom the chromosomal breakage test was inconclusive. Furthermore, knowledge about the FA subtype is relevant for the treatment and prognosis of the patients. In addition, identification of mutations allows carrier testing in the family and will enable prenatal DNA testing and preimplantation genetic diagnosis (PGD) in future pregnancies. Finally, this information can be used to rule out FA in potential donors for bone marrow transplantation.Although simultaneous testing of all FA genes by next generation sequencing will be possible in the near future, this technique will not be available immediately for all laboratories worldwide. In addition, in populations with strong founder mutations, a limited test using Sanger sequencing and MLPA will be a cost-effective alternative [33]. The strategy outlined below has been developed at our DNA diagnostics laboratory to provide a molecular diagnosis of FA. It is recognized that mutations in FANCA account for 60–70% of all FA cases and that about 15–20% of the mutations in this gene are large deletions [33, 34]. Therefore, DNA testing usually starts with a screen for deletions in FANCA. However, depending on the circumstances strategies may differ from case to case.


### 2.1. Materials

Genomic DNA (from e.g., leukocytes or fibroblasts derived from the proband or the parents) is adequate for most mutation screening assays. Screening on cDNA is more efficient but has several drawbacks: for high-quality cDNA, growing cells (stimulated leukocytes, lymphoblastoid cell lines, or fibroblasts) are necessary. In addition, common alternative splice variants will hamper the evaluation of DNA sequences. Therefore, screening on gDNA is the preferred method for mutation screening. However, during the diagnostic process, growing cells from the proband will be helpful in a couple of situations. Growing cells are indispensable for studying the effect of unclassified variants on splicing or to verify the disease gene by functional complementation of the cellular phenotype with a construct expressing a wild type copy of the suspected gene [35–37]. Finally, if no mutations can be de detected, growing cells can be used to reconfirm the diagnosis FA by checking MMC sensitivity in cell growth or G2-arrest assays [38, 39].


### 2.2. Mutation Screening Strategy

#### 2.2.1. Hints from Ethnic Background or Phenotype

Information on the ethnic background of the proband may provide a clue for a specific pathogenic mutation that most likely causes the disease, such as c.711 + 4A > T (IVS4 + 4A > T) inFANCC, a mutation present in homozygous state in 80% of all FA cases of Ashkenazi Jewish ancestry, and c.295C > T in FANCA, which was present homozygously in all 40 FA cases of Spanish Gypsy ancestry so far investigated. More examples of recurrent mutations are shown in Table 3. The distinct clinical phenotype of D1 and N patients (severely affected, often combined with leukemia or solid tumors below the age of 5 years) may provide a clue to favor BRCA2/FANCD1and PALB2/FANCN as the first gene to be screened [40–44]. This is especially worthwhile if confirmed by the cellular phenotype: in contrast to cells from all other known FA subtypes, cells from D1, N and O patients are unable to form RAD51 foci upon exposure to X rays or MMC [43–45].Table 3
Mutations detected in a cohort of 54 patients by screeningFANCA, FANCC, FANCE, FANCF and FANCG.
Allele 1Allele 2Country of origin1GeneDNA changeEffectNumber of database entriesDNA changeEffectNumber of database entries1ESFANCAex16_17deldel12xc.1115_1118delp.Val372fs62x2PTFANCAc.718C>Tp.Gln240X2xc.2870G>AW957X1x3NLFANCAex15deldel3xex15deldel3x4NLFANCAc.3788_3790delp.Phe1263del215xc.3788_3790delp.Phe1263del215x5CAFANCAc.718C>TpGlnx240X2xc.1085T>Cp.Leu362Pronovel6PTFANCAc.3788_3790delp.Phe1263del215xc.4130C>Gp.Ser1377X1x7IEFANCAc.2812_2830dupp.Asp944fs3xc.2812_2830dupp.Asp944fs3x8AUFANCAc.2303T>Cp.Leu768Pro5xc.2303T>Cp.Leu768Pro5x9NLFANCAc.862G>Tp.Glu288X1xc.862G>Tp.Glu288X1x10NLFANCAex11_33deldel1xc.2121delCp.Asn707fsnovel11DKFANCAex1_8deldel1xc.3788_3790delp.Phe1263del215x12UKFANCAc.337_338delp.Ala114fs1xc.3349A>Gp.Arg1117Gly2x13UKFANCAc.3568C>Tp.Gln1190Xnovelc.3568C>Tp.Gln1190Xnovel14NLFANCAc.487delCp.Arg163fs1xc.2851C>Tp.Arg951Trp11x15SEFANCAc.88delGp.Val30fsnovelc.100A>Tp.Lys34X2x16NLFANCAc.862G>Tp.Glu288X9xc.1771C>Tp.Arg591X9x17PTFANCAc.1709_1715+4delp.Glu570fsnovelc.3430C>Tp.Arg1144Trpnovel18NOFANCAc.100A>Tp.Lys34X2xc.1378C>Tp.Arg460Xnovel19PTFANCAex15_17deldel2xex15_17deldel2x20NLFANCAc.2982-192A>Gsplice2novelex7_31deldel21AUFANCAc.427-8_427-5delsplicenovelc.1771C>Tp.Arg591X9x22AUFANCAc.3491C>Tp.Pro1164Leunovelc.3491C>Tp.Pro1164Leunovel23CAFANCAex4_29deldelnovelex31deldel6x24NLFANCAc.3391A>Gp.Thr1131Ala15xc.3391A>Gp.Thr1131Ala15x25GRFANCAc.2T>Cp.Met1?1xc.3788_3790delp.Phe1263del215x26IEFANCAc.851dupp.Val285fsnovelc.2534T>Cp.Leu845Pro4x27NLFANCAc.2852G>Ap.Arg951Gln6xc.3624C>Tp.= (splice)2x28AUFANCAc.331_334dupp.Leu112fsnovelex22_29deldelnovel29NLFANCAc.862G>Tp.Glu288X9xc.3920delAp.Gln1307fs2x30IRFANCAex21deldelnovelex21deldelnovel31SEFANCAex1_12deldelnovelex22_29deldelnovel32NLFANCBc.755_767delp.Leu252fsnovel———33NLFANCCc.67delGp.Asp23fs50xc.553C>Tp.Arg185X14x34NLFANCCc.67delGp.Asp23fs50xc.67delGp.Asp23fs50x35CAFANCCc.67delGp.Asp23fs50xc.553C>Tp.Arg185X14x36NLFANCCc.67delGp.Asp23fs50xc.1155-1G>Csplicenovel37NLFANCCc.67delGp.Asp23fs50xc.67delGp.Asp23fs50x38NLFANCCc.67delGp.Asp23fs50xc.467delCp.Ser156fsnovel39PTFANCEc.1111C>Tp.Arg371Trp6xc.1111C>Tp.Arg371Trp6x40UKFANCFc.496C>Tp.Gln166X4xc.496C>Tp.Gln166X4x41UKFANCGc.307+2delTsplicenovelc.307+2delTsplicenovel42UKFANCGc.1471_1473delinsGp.Lys491fsnovelc.1471_1473delinsGp.Lys491fsnovel43NLFANCGc.65G>Cp.Arg22Pro6xc.65G>C;p.Arg22Pro6x44IRFANCGc.307+1G>Csplice21xc.307+1G>Csplice21x45NLFANCGc.85-1G>Asplicenovelc.85-1G>Asplicenovel1Country of origins: AU: Australia; CA: Canada; DK: Denmark; ES: Spain; GR: Greece; IE: Ireland; IR: Iran; NL: Netherlands; PT: Portugal; SE: Sweden; UK: United KingdomNumber of database entries refers to the FA database at:http://www.rockefeller.edu/fanconi/.The pathogenic state of novel missense mutations is based uponin silico prediction algorithms (SIFT, POLYPHEN2, Align GVGD), the presence of a second clearly pathogenic mutation in the same gene and segregation in the family.2Effect c.2982-192A>G: by studying cDNA it was shown that the mutation created a new splice donor site resulting in an aberrant mRNA.


#### 2.2.2. No Clues Available

(1)
In the absence of any clue to the disease gene, mutation screening starts with a search for deletions inFANCA, as this type of mutation accounts for 40% of all mutant FANCA alleles. The quantitative multiplex ligation-dependent probe amplification (MLPA) method [46] is used for this initial screen, which identifies FANCA as the most likely disease gene in 1 out of 4 patients by the detection of a—usually hemizygous-deletion. In parallel, the FANCA gene is completely sequenced. The combination of these two approaches identifies 60–70% of all FA patients as FA-A.(2)
Next,FANCC, -E, -F, and -G are screened by DNA sequencing.(3)
Only if the proband is a male,FANCB is screened by MLPA and DNA sequencing,In Table4, optimized conditions are provided for the PCR amplification of FANCA, -C, -E, -F, -G, and -B. Most PCRs can be performed under standard conditions. The PCR primers have M13 extensions which allow sequencing of all fragments with universal sequencing primers. MLPA was performed according to the instructions of the supplier. Detailed information about the sequences of the MLPA probes is available from the website of the supplier (http://www.mlpa.com). In a well-equipped laboratory with sufficient dedicated personal, testing of FANCA, -C, -E, -F, -G and -B can be completed within 1-2 weeks.Table 4
Primers and conditions for PCR on genomic DNA of the coding sequence plus intron/exon boundaries ofFANCA, FANCC, FANCE, FANCF, FANCG,andFANCB.
(a)FANCAPrimer nameSequence (5′ > 3′)Product length (bp)FANCA_ex1Fgtaaaacgacggccag GCGCCTCCCCCAGGACCAACA362FANCA_ex1Rcaggaaacagctatga AGGCTCTGGCGGGAAGGGATCGGFANCA_ex2Fgtaaaacgacggccag CTCTTCGGGAGGGTGTCGCTGGT328FANCA_ex2Rcaggaaacagctatga CTCTTCGGGAGGGTGTCGCTGGTFANCA_ex3Fgtaaaacgacggccag GCCTGGCCTGGAGCTTGAAT392FANCA_ex3Rcaggaaacagctatga CGCAGGTTGAATCAGACGCTGTTFANCA_ex4Fgtaaaacgacggccag TAAGGCATTTTAAACAGCAAGTC430FANCA_ex4Rcaggaaacagctatga TGCCAATAAATACTGAGCAAACTFANCA_ex5Fgtaaaacgacggccag AGTATTGTTTCAGGTAATTTGTT356FANCA_ex5Rcaggaaacagctatga TGAAGGTACTTCTTTCCAATCCAFANCA_ex6Fgtaaaacgacggccag AGATGTGTTTCAGGCTCTAAGTT402FANCA_ex6Rcaggaaacagctatga GCAATGCAATCTAGTCTAGTACAFANCA_ex7Fgtaaaacgacggccag TGGGATTTAGTTGAGCCTTACGTCTGC421FANCA_ex7RcaggaaacagctatgaAAGGTGAATGGAAACACTTAAACTCATGTCAFANCA_ex8Fgtaaaacgacggccag GTGGTCAGGTGAGCAGTAACTTC401FANCA_ex8Rcaggaaacagctatga TAAATAGGTACAAACAGCACGTTFANCA_ex9Fgtaaaacgacggccag TTCTCTTGTGTGATGCAGGTATC332FANCA_ex9Rcaggaaacagctatga TGACCCACAGATTCATGAGGTATFANCA_ex10Fgtaaaacgacggccag TTTTGATTAAGGCCTACAGATTG406FANCA_ex10Rcaggaaacagctatga CCTCCTCCTCACGCACGTTATCGFANCA_ex11Fgtaaaacgacggccag TTTCAAGTCTGTGGTTATAGTGG410FANCA_ex11Rcaggaaacagctatga AGACGTAAAAGAGGTCCTAGAATFANCA_ex12Fgtaaaacgacggccag CTGTGGGGCTGGTCCTTAACAAA236FANCA_ex12Rcaggaaacagctatga AGGCAGCATGACAAGTACTAGGCFANCA_ex13Fgtaaaacgacggccag ACATTGGTTTGCTTGGATATTGA377FANCA_ex13Rcaggaaacagctatga CTGACAAAGAATGTTCCATCGACFANCA_ex14Fgtaaaacgacggccag TGCTGTAATTGCTGTGTAGTCTT411FANCA_ex14Rcaggaaacagctatga ACTCACATGACAGAGAATCAGGTFANCA_ex15Fgtaaaacgacggccag ACTACAGCAGCCGCCCGGACACT430FANCA_ex15Rcaggaaacagctatga GCAGATCTGCAGGAGGCTCTTGGFANCA_ex16Fgtaaaacgacggccag TCCCAGGCAGTTCCCAGACTAAC312FANCA_ex16Rcaggaaacagctatga AGCTGATGACAAATCCTCGTAGAFANCA_ex17Fgtaaaacgacggccag ACCGCTCCCTCCTCACAGACTAC334FANCA_ex17Rcaggaaacagctatga AAGGCTGAAAAACTCAACTCAAGFANCA_ex18Fgtaaaacgacggccag GCGCACAGCATGTGGGCCTTTAC397FANCA_ex18Rcaggaaacagctatga GCAGCTGCTAGAGGCCTTTTCGGFANCA_ex19Fgtaaaacgacggccag GTGCACAAGAAGACTTCATAATG284FANCA_ex19Rcaggaaacagctatga AGTCCTTGCTTTCTACACAACTGFANCA_ex20Fgtaaaacgacggccag CTTCTCTGTGTTGCAGCATATTC298FANCA_ex20Rcaggaaacagctatga AGAAGAAACCTGGAAGTAGTCATFANCA_ex21Fgtaaaacgacggccag ATAATAGATTTGGGGATTGTAAT255FANCA_ex21Rcaggaaacagctatga CAACAGACACTCAAGGTTAGGAAFANCA_ex22Fgtaaaacgacggccag TGCAGTGAAGAGTCCTGTTGAGT305FANCA_ex22Rcaggaaacagctatga ACACACCAGCCTGATGTCACTATFANCA_ex23Fgtaaaacgacggccag CAGTCAGCAGGATCCGTGGAATC416FANCA_ex23Rcaggaaacagctatga GGCCCTGGAACATCTGATACGACFANCA_ex24Fgtaaaacgacggccag CCTTCCTGCTGCTCCCGTCC229FANCA_ex24Rcaggaaacagctatga CAGACTTGGCCCAGCAAGAGFANCA_ex25Fgtaaaacgacggccag CCGCTGGTGGTTGGATTAGCTGT296FANCA_ex25Rcaggaaacagctatga TTTCCAGGGCACTGAAGACGAATFANCA_ex26Fgtaaaacgacggccag AGCTTGGAAGAGGGCAGTCTGCT347FANCA_ex26Rcaggaaacagctatga CTCTTCTAATTTTATCAAACGAGFANCA_ex27Fgtaaaacgacggccag AGACTGTCTCACAACAAACGAAC356FANCA_ex27Rcaggaaacagctatga CGGTCCGAAAGCTGCGTAAACFANCA_ex28Fgtaaaacgacggccag GTTGATGGTCTGTTTCCACCTGA401FANCA_ex28Rcaggaaacagctatga GAAGGAACGGTCACCTACGTGCTFANCA_ex29Fgtaaaacgacggccag GACATGGAGGACTGCGTATGAGA411FANCA_ex29Rcaggaaacagctatga GTGGCTGTGATGACTGGAACGTGFANCA_ex30Fgtaaaacgacggccag CCCGAGCCGCCAGTCTCAACCCA411FANCA_ex30Rcaggaaacagctatga AAAGGCAGACCCACCCTAAGCTAFANCA_ex31Fgtaaaacgacggccag GATAAGCCTCCTTGGTCATGGTA406FANCA_ex31Rcaggaaacagctatga TGGCAATAAATATCTTAATAGCAFANCA_ex32Fgtaaaacgacggccag TTCCTGTGCCAGCATACTGCTCT359FANCA_ex32Rcaggaaacagctatga GGGTGGGGACACACAGACAAGTAFANCA_ex33Fgtaaaacgacggccag TGGGTTTCAGGGTGGTGGTTGCT356FANCA_ex33Rcaggaaacagctatga GAACCCTTTCCTCAGTAATTCACFANCA_ex34Fgtaaaacgacggccag CGCCCAGGGAAGCCGTTAAGTTT333FANCA_ex34Rcaggaaacagctatga GCGTTCTGAGAAGGCCACGAGAGFANCA_ex35Fgtaaaacgacggccag TTCCTTCACTCTACTAGTTGTGG311FANCA_ex35Rcaggaaacagctatga TGAGATGGTAACACCCGTGATGGFANCA_ex36Fgtaaaacgacggccag CCATCTCAGCCACCCTCATCTGT350FANCA_ex36Rcaggaaacagctatga AGGCGCCCACCACCACGAGAACTFANCA_ex37Fgtaaaacgacggccag GACTTGGTTTCTATGGCGTGGTT310FANCA_ex37Rcaggaaacagctatga CCCAGAGAAATAGCACTGATTGAFANCA_ex38Fgtaaaacgacggccag GTTTTCTAAGATCCACTTAAAGG362FANCA_ex38Rcaggaaacagctatga CTCACTCACACTTCCGCAAACACFANCA_ex39Fgtaaaacgacggccag CTGTCCAGAGGCCCAGTATTACC387FANCA_ex39Rcaggaaacagctatga AGGAGGGCTCGTTCTTAACCATTFANCA_ex40Fgtaaaacgacggccag GGTGTCCCCAGCACTGATAATAG353FANCA_ex40Rcaggaaacagctatga AGACATAGTGACAAATGGCTACAFANCA_ex41Fgtaaaacgacggccag CCCTTGGCATCACCTGCTACCTT403FANCA_ex41Rcaggaaacagctatga AACAGGCAAACTCACAGGTTAGAFANCA_ex42Fgtaaaacgacggccag ACCAGCCCTGTTTCTGTATGTCT248FANCA_ex42Rcaggaaacagctatga ACATGGCCCAGGCAGCTGTCAATFANCA_ex43Fgtaaaacgacggccag TGTGGGGGACATGAGAATTGACA378FANCA_ex43Rcaggaaacagctatga GTAATCCACTTTTTAGTGCAACAFANCAIVS10Fgtaaaacgacggccag TTTACATGTGCATCAGTTAGCTT184FANCAIVS10Rcaggaaacagctatga CATGAAGACACAGAAAAAGTAGGT(b)FANCCPrimer nameSequence (5′ > 3′)Product length (bp)FANCC_ex1FFANCC_ex1Rgtaaaacgacggccag ACCATTTCCTTCAGTGCTGGACAcaggaaacagctatga CCATCGGCACTTCAGTCAATACC378FANCC_ex2FFANCC_ex2Rgtaaaacgacggccag CTAAACAAGAAGCATTCACGTTCcaggaaacagctatga GGAGAAAGGTTCATAATGTAAGC303FANCC_ex3FFANCC_ex3Rgtaaaacgacggccag TCAGCAGAAAGAGAATGTGCAAAcaggaaacagctatga AACATCATAGAACTGGATTCCAC405FANCC_ex4FFANCC_ex4Rgtaaaacgacggccag TGTACATAAAAGGCACTTGCATTcaggaaacagctatga TCCCATCTCACATTTCTTCCGTA380FANCC_ex5FFANCC_ex5Rgtaaaacgacggccag AGAACTGATGTAATCCTGTTTGCcaggaaacagctatga TTACTGCTCTGTGAGAGTTGAGA367FANCC_ex6FFANCC_ex6Rgtaaaacgacggccag GTCTTTGACCTTTTTAGCATGAAcaggaaacagctatga AACGTTTGGACACTGCTGTCGTA387FANCC_ex7FFANCC_ex7Rgtaaaacgacggccag ATTAGTGATTGCATTTTGAACTTcaggaaacagctatga CAAAAATAAAATGTAAATACACG422FANCC_ex8FFANCC_ex8Rgtaaaacgacggccag CTCCTTTGGCTGATAATAGCAAGcaggaaacagctatga CTGATTTTTGAGTTTTTACCTCT336FANCC_ex9FFANCC_ex9Rgtaaaacgacggccag ATACTGCTGAAGCTTATGGCACAcaggaaacagctatga TAACCTTTGTTGGGGCACTCATT400FANCC_ex10FFANCC_ex10Rgtaaaacgacggccag TATGAGGTTATTGGGAGCTTATTcaggaaacagctatga CTGTCTCCCTCATGCTGTAGATA382FANCC_ex11FFANCC_ex11Rgtaaaacgacggccag GAACCAGAAGTAAAGGGCGTCTCcaggaaacagctatga CTGACCTGCTCCAAGCCATCCGT416FANCC_ex12FFANCC_ex12Rgtaaaacgacggccag AAGTACAATTTAAGCCAACCGTTcaggaaacagctatga AGGTTGCCATGACATATGCCATC451FANCC_ex13FFANCC_ex13Rgtaaaacgacggccag CCTCTCTCAGGGGCCAGTGCTTAcaggaaacagctatga AGACCCTCGGACAGGTAACCCAC435FANCC_ex14FFANCC_ex14Rgtaaaacgacggccag ACTTGCTATGCTAATCACCTTGCcaggaaacagctatga AATGCGTGGCCACAGGTCATCAC437(c)FANCEPrimer nameSequence (5′ > 3′)Product length (bp)FANCE_ex1FFANCE_ex1Rgtaaaacgacggccag CGCCTCCCTCCTTCCCTTTCcaggaaacagctatga CCCGCCTCCCATACCTGCTAA540FANCE_ex2aFFANCE_ex2aRgtaaaacgacggccag GCTCTGCCCAGTCTGCCTTGTGCcaggaaacagctatga CTCTGAGTCCTTTCTGCGTTTCC469FANCE_ex2bFFANCE_ex2bRgtaaaacgacggccag GCCAGAGACAGCTCCAAAGTCTAcaggaaacagctatga CAGCCTTCCCCATGGATAAAGCC479FANCE_ex3FFANCE_ex3Rgtaaaacgacggccag GCCTCTTGACTTTCTTGAATCATcaggaaacagctatga ACTGTCCTCAGACCTTTACTCCA352FANCE_ex4FFANCE_ex4Rgtaaaacgacggccag TTGAACCAAGTGTAGACTTACCAcaggaaacagctatga GGGAAGGAACCAAGGGCTAAAAG436FANCE_ex5FFANCE_ex5Rgtaaaacgacggccag GTATCTTTTAGCCCTTGGTTCCTcaggaaacagctatga GAATCCCCTCTCTCAAGTACCAC431FANCE_ex6FFANCE_ex6Rgtaaaacgacggccag TTTCCTTTGTAACATGTATCATCcaggaaacagctatga AGCAGAAAGCAGGGAGGCGGTAA433FANCE_ex7FFANCE_ex7Rgtaaaacgacggccag ACAGGCTGGGCATTCTGTTACCGcaggaaacagctatga AGTGAGACACAAGGATCCCCTAA425FANCE_ex8FFANCE_ex8Rgtaaaacgacggccag TTGGAGCAGCAGATAGATACTCAcaggaaacagctatga AGAGGTGGAGCTGAAGTGACCAT380FANCE_ex9FFANCE_ex9Rgtaaaacgacggccag GTTACCTGCCCAGGGTCACCTAGcaggaaacagctatga CTGGCCAGCACTCAGGGTTTTAT388FANCE_ex10FFANCE_ex10Rgtaaaacgacggccag TGGCCTCCTCTCTCCTCAATAGAcaggaaacagctatga AACAGGGAGGCAGTTGCAATCTG369(d)FANCFPrimer nameSequence (5′ > 3′)Product length (bp)FANCF_ex1aFFANCF_ex1aRgtaaaacgacggccag TTTCGCGGATGTTCCAATCAGTAcaggaaacagctatga CTGCACCAGGTGGTAACGAGCTG449FANCF_ex1bFFANCF_ex1bRgtaaaacgacggccag AGTGGAGGCAAGAGGGCGGCTTTcaggaaacagctatga GCTATCACCTTCAGGAAGTTGTT456FANCF_ex1cFFANCF_ex1cRgtaaaacgacggccag CCCAAATCTCCAGGAGGACTCTCcaggaaacagctatga TTTCTGAAGGTCATAGTGCAAAC444FANCF_ex1dFFANCF_ex1dRgtaaaacgacggccag GCTTTTGACTTTAGTGACTAGCCcaggaaacagctatga ATTTGGTGAGAACATTGTAATTT456(e)FANCGPrimer nameSequence (5′ > 3′)Product length (bp)FANCG_ex1FFANCG_ex1Rgtaaaacgacggccag AGCCTGGGCGGGTGGATTGGGACcaggaaacagctatga TCATTTCTGGCTCTTTGGTCAAG389FANCG_ex2FFANCG_ex2Rgtaaaacgacggccag CAGGCCAAGGTAACACGGTTGCTcaggaaacagctatga CCAGTCTCCTCTGTGCCTTAAAC460FANCG_ex3FFANCG_ex3Rgtaaaacgacggccag TATTGTAGCTGTTTTGGTTGGAGcaggaaacagctatga GGTGACAGATGTTGTTTATCCTC362FANCG_ex4FFANCG_ex4Rgtaaaacgacggccag GGAGATGGAGGATGAGGTGCTACcaggaaacagctatga CGACCACCAACCCAGCCGCCTGT411FANCG_ex5FFANCG_ex5Rgtaaaacgacggccag AGATGGAGATAGGAGAAGACGAGcaggaaacagctatga GCTTCATGAAGGCTGCTTAGTGC454FANCG_ex6FFANCG_ex6Rgtaaaacgacggccag CAGTTCCATGGGCTTCTTAGACCcaggaaacagctatga TCAGGGCTGCAACCAAGTACAAC393FANCG_ex7FFANCG_ex7Rgtaaaacgacggccag GCACTGGGGTCCTGTCACCGTAAcaggaaacagctatga ATAATCTTTGGGAGCCATACTTC418FANCG_ex8FFANCG_ex8Rgtaaaacgacggccag GCTTGTGATGGGGTGACTTGACTcaggaaacagctatga AGTTCAGGTCTAGAAGCAAGGTA438FANCG_ex9FFANCG_ex9Rgtaaaacgacggccag CCTCCTCAGGGCCCATGAACATCcaggaaacagctatga GCAGTGTCTTGAAAGGCATGAGC400FANCG_ex10FFANCG_ex10Rgtaaaacgacggccag CAGGACTCTGCATGGTACCAGcaggaaacagctatga CCAATCAGAAAATCATCCCTC460FANCG_ex11FFANCG_ex11Rgtaaaacgacggccag AGCTCCATGTTCACCTACTTACCcaggaaacagctatga CAGTGCCGCATCTGACTTACATC397FANCG_ex12FFANCG_ex12Rgtaaaacgacggccag AGGATTTGGGGTTTTGGTGACTGcaggaaacagctatga AACTCTTGGGAGCCCTGCATACA445FANCG_ex13FFANCG_ex13Rgtaaaacgacggccag CCGCTTCCATATGTGAGTGTAGGcaggaaacagctatgaC CACAATAGGTCCAAGGACTCTA340FANCG_ex14FFANCG_ex14Rgtaaaacgacggccag CCAAACTAAGGGGTCACATGAAGcaggaaacagctatga GATGGTGAAGCAGAAAGCCCTCC405(f)FANCBPrimer nameSequence (5′ > 3′)Product length (bp)FANCB_ex3AFFANCB_ex3ARgtaaaacgacggccag GATATGGTTATTTGAATTCTTAGCAcaggaaacagctatga GCCATCCTTCATCTCATAGCCTAGT721FANCB_ex3BFFANCB_ex3BRgtaaaacgacggccag ATTAACCTCCCTTACATTGTGATAGcaggaaacagctatga CAATAAGACTCCAGAATGAACTCTA811FANCB_ex4FFANCB_ex4Rgtaaaacgacggccag TTTACAAATGACAACTACATGAcaggaaacagctatga TTAAGTATAAAACCACCAATAT391FANCB_ex5FFANCB_ex5Rgtaaaacgacggccag ACTGCATCTGGCCTATAGTTcaggaaacagctatga AATACCATTTTTACCCAAGC411FANCB_ex6FFANCB_ex6Rgtaaaacgacggccag GTATTTCCTGAATTATTGGTATGTCcaggaaacagctatga CATAAAAGTCCACCATTATAACCTC395FANCB_ex7FFANCB_ex7Rgtaaaacgacggccag TGTTTGGGCCATAAGCCCTAcaggaaacagctatga  TTCTGGAGCATCAAGACAGT355FANCB_ex8FFANCB_ex8Rgtaaaacgacggccag GTTGTTTGTATGACATTTAATCATCcaggaaacagctatga ATCATTAAACTCTGCCCATTATCAG636FANCB_ex9FFANCB_ex9Rgtaaaacgacggccag AGGTAATTTTGTTGGCACTTcaggaaacagctatga ATGCGTTCATTCATGCTAGG531FANCB_ex10FFANCB_ex10Rgtaaaacgacggccag AATTGGTTCTGTTTATCATTATGGTcaggaaacagctatga CTACTACAGTAAGCCTCGGTGTTTA686PCR conditions:PCR was performed in Applied Biosystems PE9700 system using 96-well plates. PCR reactions (final volume 25μl) contained 0.5 units Platinum Taq polymerase (Invitrogen), 1,5 mM MgCl2, 0.2 mM NTPs (Invitrogen), and 10 pmol primer.For the large majority of amplicons, standard PCR conditions were used: preheat 95°C, 5 min, denaturation 95°C, 30 sec, annealing 60°C, 30 sec., elongation 72°C, 1 min, number of cycles: 33.Fragments with a different annealing temperature wereFANCA exons 5, 7, 13, 21, 26, 31, and 38, FANCC exon 7, FANCF fragment 1d and FANCE exon 1 : 55°C; FANCA exon  1 : 64°C. For FANCE exon 1 the PCR mix was supplemented with 10% DMSO.ForFANCB different PCR conditions were used: preheat 95°C, 5 min, denaturation 95°C, 1 min, annealing 50°C, 1 min., elongation 72°C, 1 min., number of cycles 30. For FANCB exon 7 and 9 the annealing temperature was 55°C. For sequencing of exon 7 forward, a special sequencing primer was used: 5′-TTTTTAGAAGGAATGTCTTG-3′.FA gene specific part of the primer is indicated in capitals. Primers are extended with M13 sequence (indicated in normal letter type), which is used for the sequencing reaction.After screeningFANCA, -C, -E, -F, -G, and –B, a molecular diagnosis is obtained for ~85% of the patients [34]. In our cohort of 54 patients, referred to our diagnostic service since 2008, mutations were detected in 45 patients (83%). FANCA mutations were found in 31 of the patients (57%), FANCC mutations in 6 patients (11%), and FANCG mutations in 5 patients (9%). FANCB, FANCE, and FANCF mutations were found in single families (Table 3). In the small group of patients without mutations no complementation analysis or FANCD2 western blotting was performed. Therefore, we do not know if we missed FANCA, -C, -E, -F, -G, and -B mutations in these patients or that these patients have mutations in other FA genes. Table 3 does not include prenatal cases, because prenatal testing is only offered in couples in which the FA-causing mutations are already established. Testing was offered as a diagnostic service for which a fee was charged.For the patients negative forFANCA, -C, -E, -F, -G, and -B mutations, next generation sequencing can be used to analyze all other FA genes. If this technique is not available, further analysis will depend on the availability of growing cells from the proband. In that case a western blot should reveal whether both FANCD2 isoforms are present at normal levels.(1)
If both FANCD2 bands are absent or very weak,FANCD2is sequenced. Because of the presence of FANCD2 pseudogene sequences in the genome, this testing must be performed on cDNA or gDNA using specially designed primers [26].(2)
If only the short isoform of FANCD2 is present,FANCL and FANCM are sequenced. If no mutations are found, the patient may be mutated in FANCI or in another unidentified FA gene acting upstream of FANCD2.(3)
If both isoforms are present, and if the clinical phenotype is compatible with FA-D1 or FA-N,BRCA2/FANCD1 and PALB2/FANCN are screened by MLPA and DNA sequencing.(4)
If negative,BRIP1/FANCJ, PALB2/FANCN, RAD51C/FANCO, and SLX4/FANCP are sequenced.(5)
If negative again, the patient should be screened for mutations inNBS1, ESCO2 and DDX11 to test for Nijmegen breakage syndrome, Roberts syndrome and Warsaw Breakage syndrome, respectively [47, 48]. The latter two syndromes can also be excluded by analyzing metaphase spreads for sister chromatid cohesion defects. If again negative, the patient is likely to be mutated in a novel FA gene acting downstream of FANCD2 ubiquitination.


## 2.1. Materials

Genomic DNA (from e.g., leukocytes or fibroblasts derived from the proband or the parents) is adequate for most mutation screening assays. Screening on cDNA is more efficient but has several drawbacks: for high-quality cDNA, growing cells (stimulated leukocytes, lymphoblastoid cell lines, or fibroblasts) are necessary. In addition, common alternative splice variants will hamper the evaluation of DNA sequences. Therefore, screening on gDNA is the preferred method for mutation screening. However, during the diagnostic process, growing cells from the proband will be helpful in a couple of situations. Growing cells are indispensable for studying the effect of unclassified variants on splicing or to verify the disease gene by functional complementation of the cellular phenotype with a construct expressing a wild type copy of the suspected gene [35–37]. Finally, if no mutations can be de detected, growing cells can be used to reconfirm the diagnosis FA by checking MMC sensitivity in cell growth or G2-arrest assays [38, 39].


## 2.2. Mutation Screening Strategy

### 2.2.1. Hints from Ethnic Background or Phenotype

Information on the ethnic background of the proband may provide a clue for a specific pathogenic mutation that most likely causes the disease, such as c.711 + 4A > T (IVS4 + 4A > T) inFANCC, a mutation present in homozygous state in 80% of all FA cases of Ashkenazi Jewish ancestry, and c.295C > T in FANCA, which was present homozygously in all 40 FA cases of Spanish Gypsy ancestry so far investigated. More examples of recurrent mutations are shown in Table 3. The distinct clinical phenotype of D1 and N patients (severely affected, often combined with leukemia or solid tumors below the age of 5 years) may provide a clue to favor BRCA2/FANCD1and PALB2/FANCN as the first gene to be screened [40–44]. This is especially worthwhile if confirmed by the cellular phenotype: in contrast to cells from all other known FA subtypes, cells from D1, N and O patients are unable to form RAD51 foci upon exposure to X rays or MMC [43–45].Table 3
Mutations detected in a cohort of 54 patients by screeningFANCA, FANCC, FANCE, FANCF and FANCG.
Allele 1Allele 2Country of origin1GeneDNA changeEffectNumber of database entriesDNA changeEffectNumber of database entries1ESFANCAex16_17deldel12xc.1115_1118delp.Val372fs62x2PTFANCAc.718C>Tp.Gln240X2xc.2870G>AW957X1x3NLFANCAex15deldel3xex15deldel3x4NLFANCAc.3788_3790delp.Phe1263del215xc.3788_3790delp.Phe1263del215x5CAFANCAc.718C>TpGlnx240X2xc.1085T>Cp.Leu362Pronovel6PTFANCAc.3788_3790delp.Phe1263del215xc.4130C>Gp.Ser1377X1x7IEFANCAc.2812_2830dupp.Asp944fs3xc.2812_2830dupp.Asp944fs3x8AUFANCAc.2303T>Cp.Leu768Pro5xc.2303T>Cp.Leu768Pro5x9NLFANCAc.862G>Tp.Glu288X1xc.862G>Tp.Glu288X1x10NLFANCAex11_33deldel1xc.2121delCp.Asn707fsnovel11DKFANCAex1_8deldel1xc.3788_3790delp.Phe1263del215x12UKFANCAc.337_338delp.Ala114fs1xc.3349A>Gp.Arg1117Gly2x13UKFANCAc.3568C>Tp.Gln1190Xnovelc.3568C>Tp.Gln1190Xnovel14NLFANCAc.487delCp.Arg163fs1xc.2851C>Tp.Arg951Trp11x15SEFANCAc.88delGp.Val30fsnovelc.100A>Tp.Lys34X2x16NLFANCAc.862G>Tp.Glu288X9xc.1771C>Tp.Arg591X9x17PTFANCAc.1709_1715+4delp.Glu570fsnovelc.3430C>Tp.Arg1144Trpnovel18NOFANCAc.100A>Tp.Lys34X2xc.1378C>Tp.Arg460Xnovel19PTFANCAex15_17deldel2xex15_17deldel2x20NLFANCAc.2982-192A>Gsplice2novelex7_31deldel21AUFANCAc.427-8_427-5delsplicenovelc.1771C>Tp.Arg591X9x22AUFANCAc.3491C>Tp.Pro1164Leunovelc.3491C>Tp.Pro1164Leunovel23CAFANCAex4_29deldelnovelex31deldel6x24NLFANCAc.3391A>Gp.Thr1131Ala15xc.3391A>Gp.Thr1131Ala15x25GRFANCAc.2T>Cp.Met1?1xc.3788_3790delp.Phe1263del215x26IEFANCAc.851dupp.Val285fsnovelc.2534T>Cp.Leu845Pro4x27NLFANCAc.2852G>Ap.Arg951Gln6xc.3624C>Tp.= (splice)2x28AUFANCAc.331_334dupp.Leu112fsnovelex22_29deldelnovel29NLFANCAc.862G>Tp.Glu288X9xc.3920delAp.Gln1307fs2x30IRFANCAex21deldelnovelex21deldelnovel31SEFANCAex1_12deldelnovelex22_29deldelnovel32NLFANCBc.755_767delp.Leu252fsnovel———33NLFANCCc.67delGp.Asp23fs50xc.553C>Tp.Arg185X14x34NLFANCCc.67delGp.Asp23fs50xc.67delGp.Asp23fs50x35CAFANCCc.67delGp.Asp23fs50xc.553C>Tp.Arg185X14x36NLFANCCc.67delGp.Asp23fs50xc.1155-1G>Csplicenovel37NLFANCCc.67delGp.Asp23fs50xc.67delGp.Asp23fs50x38NLFANCCc.67delGp.Asp23fs50xc.467delCp.Ser156fsnovel39PTFANCEc.1111C>Tp.Arg371Trp6xc.1111C>Tp.Arg371Trp6x40UKFANCFc.496C>Tp.Gln166X4xc.496C>Tp.Gln166X4x41UKFANCGc.307+2delTsplicenovelc.307+2delTsplicenovel42UKFANCGc.1471_1473delinsGp.Lys491fsnovelc.1471_1473delinsGp.Lys491fsnovel43NLFANCGc.65G>Cp.Arg22Pro6xc.65G>C;p.Arg22Pro6x44IRFANCGc.307+1G>Csplice21xc.307+1G>Csplice21x45NLFANCGc.85-1G>Asplicenovelc.85-1G>Asplicenovel1Country of origins: AU: Australia; CA: Canada; DK: Denmark; ES: Spain; GR: Greece; IE: Ireland; IR: Iran; NL: Netherlands; PT: Portugal; SE: Sweden; UK: United KingdomNumber of database entries refers to the FA database at:http://www.rockefeller.edu/fanconi/.The pathogenic state of novel missense mutations is based uponin silico prediction algorithms (SIFT, POLYPHEN2, Align GVGD), the presence of a second clearly pathogenic mutation in the same gene and segregation in the family.2Effect c.2982-192A>G: by studying cDNA it was shown that the mutation created a new splice donor site resulting in an aberrant mRNA.


### 2.2.2. No Clues Available

(1)
In the absence of any clue to the disease gene, mutation screening starts with a search for deletions inFANCA, as this type of mutation accounts for 40% of all mutant FANCA alleles. The quantitative multiplex ligation-dependent probe amplification (MLPA) method [46] is used for this initial screen, which identifies FANCA as the most likely disease gene in 1 out of 4 patients by the detection of a—usually hemizygous-deletion. In parallel, the FANCA gene is completely sequenced. The combination of these two approaches identifies 60–70% of all FA patients as FA-A.(2)
Next,FANCC, -E, -F, and -G are screened by DNA sequencing.(3)
Only if the proband is a male,FANCB is screened by MLPA and DNA sequencing,In Table4, optimized conditions are provided for the PCR amplification of FANCA, -C, -E, -F, -G, and -B. Most PCRs can be performed under standard conditions. The PCR primers have M13 extensions which allow sequencing of all fragments with universal sequencing primers. MLPA was performed according to the instructions of the supplier. Detailed information about the sequences of the MLPA probes is available from the website of the supplier (http://www.mlpa.com). In a well-equipped laboratory with sufficient dedicated personal, testing of FANCA, -C, -E, -F, -G and -B can be completed within 1-2 weeks.Table 4
Primers and conditions for PCR on genomic DNA of the coding sequence plus intron/exon boundaries ofFANCA, FANCC, FANCE, FANCF, FANCG,andFANCB.
(a)FANCAPrimer nameSequence (5′ > 3′)Product length (bp)FANCA_ex1Fgtaaaacgacggccag GCGCCTCCCCCAGGACCAACA362FANCA_ex1Rcaggaaacagctatga AGGCTCTGGCGGGAAGGGATCGGFANCA_ex2Fgtaaaacgacggccag CTCTTCGGGAGGGTGTCGCTGGT328FANCA_ex2Rcaggaaacagctatga CTCTTCGGGAGGGTGTCGCTGGTFANCA_ex3Fgtaaaacgacggccag GCCTGGCCTGGAGCTTGAAT392FANCA_ex3Rcaggaaacagctatga CGCAGGTTGAATCAGACGCTGTTFANCA_ex4Fgtaaaacgacggccag TAAGGCATTTTAAACAGCAAGTC430FANCA_ex4Rcaggaaacagctatga TGCCAATAAATACTGAGCAAACTFANCA_ex5Fgtaaaacgacggccag AGTATTGTTTCAGGTAATTTGTT356FANCA_ex5Rcaggaaacagctatga TGAAGGTACTTCTTTCCAATCCAFANCA_ex6Fgtaaaacgacggccag AGATGTGTTTCAGGCTCTAAGTT402FANCA_ex6Rcaggaaacagctatga GCAATGCAATCTAGTCTAGTACAFANCA_ex7Fgtaaaacgacggccag TGGGATTTAGTTGAGCCTTACGTCTGC421FANCA_ex7RcaggaaacagctatgaAAGGTGAATGGAAACACTTAAACTCATGTCAFANCA_ex8Fgtaaaacgacggccag GTGGTCAGGTGAGCAGTAACTTC401FANCA_ex8Rcaggaaacagctatga TAAATAGGTACAAACAGCACGTTFANCA_ex9Fgtaaaacgacggccag TTCTCTTGTGTGATGCAGGTATC332FANCA_ex9Rcaggaaacagctatga TGACCCACAGATTCATGAGGTATFANCA_ex10Fgtaaaacgacggccag TTTTGATTAAGGCCTACAGATTG406FANCA_ex10Rcaggaaacagctatga CCTCCTCCTCACGCACGTTATCGFANCA_ex11Fgtaaaacgacggccag TTTCAAGTCTGTGGTTATAGTGG410FANCA_ex11Rcaggaaacagctatga AGACGTAAAAGAGGTCCTAGAATFANCA_ex12Fgtaaaacgacggccag CTGTGGGGCTGGTCCTTAACAAA236FANCA_ex12Rcaggaaacagctatga AGGCAGCATGACAAGTACTAGGCFANCA_ex13Fgtaaaacgacggccag ACATTGGTTTGCTTGGATATTGA377FANCA_ex13Rcaggaaacagctatga CTGACAAAGAATGTTCCATCGACFANCA_ex14Fgtaaaacgacggccag TGCTGTAATTGCTGTGTAGTCTT411FANCA_ex14Rcaggaaacagctatga ACTCACATGACAGAGAATCAGGTFANCA_ex15Fgtaaaacgacggccag ACTACAGCAGCCGCCCGGACACT430FANCA_ex15Rcaggaaacagctatga GCAGATCTGCAGGAGGCTCTTGGFANCA_ex16Fgtaaaacgacggccag TCCCAGGCAGTTCCCAGACTAAC312FANCA_ex16Rcaggaaacagctatga AGCTGATGACAAATCCTCGTAGAFANCA_ex17Fgtaaaacgacggccag ACCGCTCCCTCCTCACAGACTAC334FANCA_ex17Rcaggaaacagctatga AAGGCTGAAAAACTCAACTCAAGFANCA_ex18Fgtaaaacgacggccag GCGCACAGCATGTGGGCCTTTAC397FANCA_ex18Rcaggaaacagctatga GCAGCTGCTAGAGGCCTTTTCGGFANCA_ex19Fgtaaaacgacggccag GTGCACAAGAAGACTTCATAATG284FANCA_ex19Rcaggaaacagctatga AGTCCTTGCTTTCTACACAACTGFANCA_ex20Fgtaaaacgacggccag CTTCTCTGTGTTGCAGCATATTC298FANCA_ex20Rcaggaaacagctatga AGAAGAAACCTGGAAGTAGTCATFANCA_ex21Fgtaaaacgacggccag ATAATAGATTTGGGGATTGTAAT255FANCA_ex21Rcaggaaacagctatga CAACAGACACTCAAGGTTAGGAAFANCA_ex22Fgtaaaacgacggccag TGCAGTGAAGAGTCCTGTTGAGT305FANCA_ex22Rcaggaaacagctatga ACACACCAGCCTGATGTCACTATFANCA_ex23Fgtaaaacgacggccag CAGTCAGCAGGATCCGTGGAATC416FANCA_ex23Rcaggaaacagctatga GGCCCTGGAACATCTGATACGACFANCA_ex24Fgtaaaacgacggccag CCTTCCTGCTGCTCCCGTCC229FANCA_ex24Rcaggaaacagctatga CAGACTTGGCCCAGCAAGAGFANCA_ex25Fgtaaaacgacggccag CCGCTGGTGGTTGGATTAGCTGT296FANCA_ex25Rcaggaaacagctatga TTTCCAGGGCACTGAAGACGAATFANCA_ex26Fgtaaaacgacggccag AGCTTGGAAGAGGGCAGTCTGCT347FANCA_ex26Rcaggaaacagctatga CTCTTCTAATTTTATCAAACGAGFANCA_ex27Fgtaaaacgacggccag AGACTGTCTCACAACAAACGAAC356FANCA_ex27Rcaggaaacagctatga CGGTCCGAAAGCTGCGTAAACFANCA_ex28Fgtaaaacgacggccag GTTGATGGTCTGTTTCCACCTGA401FANCA_ex28Rcaggaaacagctatga GAAGGAACGGTCACCTACGTGCTFANCA_ex29Fgtaaaacgacggccag GACATGGAGGACTGCGTATGAGA411FANCA_ex29Rcaggaaacagctatga GTGGCTGTGATGACTGGAACGTGFANCA_ex30Fgtaaaacgacggccag CCCGAGCCGCCAGTCTCAACCCA411FANCA_ex30Rcaggaaacagctatga AAAGGCAGACCCACCCTAAGCTAFANCA_ex31Fgtaaaacgacggccag GATAAGCCTCCTTGGTCATGGTA406FANCA_ex31Rcaggaaacagctatga TGGCAATAAATATCTTAATAGCAFANCA_ex32Fgtaaaacgacggccag TTCCTGTGCCAGCATACTGCTCT359FANCA_ex32Rcaggaaacagctatga GGGTGGGGACACACAGACAAGTAFANCA_ex33Fgtaaaacgacggccag TGGGTTTCAGGGTGGTGGTTGCT356FANCA_ex33Rcaggaaacagctatga GAACCCTTTCCTCAGTAATTCACFANCA_ex34Fgtaaaacgacggccag CGCCCAGGGAAGCCGTTAAGTTT333FANCA_ex34Rcaggaaacagctatga GCGTTCTGAGAAGGCCACGAGAGFANCA_ex35Fgtaaaacgacggccag TTCCTTCACTCTACTAGTTGTGG311FANCA_ex35Rcaggaaacagctatga TGAGATGGTAACACCCGTGATGGFANCA_ex36Fgtaaaacgacggccag CCATCTCAGCCACCCTCATCTGT350FANCA_ex36Rcaggaaacagctatga AGGCGCCCACCACCACGAGAACTFANCA_ex37Fgtaaaacgacggccag GACTTGGTTTCTATGGCGTGGTT310FANCA_ex37Rcaggaaacagctatga CCCAGAGAAATAGCACTGATTGAFANCA_ex38Fgtaaaacgacggccag GTTTTCTAAGATCCACTTAAAGG362FANCA_ex38Rcaggaaacagctatga CTCACTCACACTTCCGCAAACACFANCA_ex39Fgtaaaacgacggccag CTGTCCAGAGGCCCAGTATTACC387FANCA_ex39Rcaggaaacagctatga AGGAGGGCTCGTTCTTAACCATTFANCA_ex40Fgtaaaacgacggccag GGTGTCCCCAGCACTGATAATAG353FANCA_ex40Rcaggaaacagctatga AGACATAGTGACAAATGGCTACAFANCA_ex41Fgtaaaacgacggccag CCCTTGGCATCACCTGCTACCTT403FANCA_ex41Rcaggaaacagctatga AACAGGCAAACTCACAGGTTAGAFANCA_ex42Fgtaaaacgacggccag ACCAGCCCTGTTTCTGTATGTCT248FANCA_ex42Rcaggaaacagctatga ACATGGCCCAGGCAGCTGTCAATFANCA_ex43Fgtaaaacgacggccag TGTGGGGGACATGAGAATTGACA378FANCA_ex43Rcaggaaacagctatga GTAATCCACTTTTTAGTGCAACAFANCAIVS10Fgtaaaacgacggccag TTTACATGTGCATCAGTTAGCTT184FANCAIVS10Rcaggaaacagctatga CATGAAGACACAGAAAAAGTAGGT(b)FANCCPrimer nameSequence (5′ > 3′)Product length (bp)FANCC_ex1FFANCC_ex1Rgtaaaacgacggccag ACCATTTCCTTCAGTGCTGGACAcaggaaacagctatga CCATCGGCACTTCAGTCAATACC378FANCC_ex2FFANCC_ex2Rgtaaaacgacggccag CTAAACAAGAAGCATTCACGTTCcaggaaacagctatga GGAGAAAGGTTCATAATGTAAGC303FANCC_ex3FFANCC_ex3Rgtaaaacgacggccag TCAGCAGAAAGAGAATGTGCAAAcaggaaacagctatga AACATCATAGAACTGGATTCCAC405FANCC_ex4FFANCC_ex4Rgtaaaacgacggccag TGTACATAAAAGGCACTTGCATTcaggaaacagctatga TCCCATCTCACATTTCTTCCGTA380FANCC_ex5FFANCC_ex5Rgtaaaacgacggccag AGAACTGATGTAATCCTGTTTGCcaggaaacagctatga TTACTGCTCTGTGAGAGTTGAGA367FANCC_ex6FFANCC_ex6Rgtaaaacgacggccag GTCTTTGACCTTTTTAGCATGAAcaggaaacagctatga AACGTTTGGACACTGCTGTCGTA387FANCC_ex7FFANCC_ex7Rgtaaaacgacggccag ATTAGTGATTGCATTTTGAACTTcaggaaacagctatga CAAAAATAAAATGTAAATACACG422FANCC_ex8FFANCC_ex8Rgtaaaacgacggccag CTCCTTTGGCTGATAATAGCAAGcaggaaacagctatga CTGATTTTTGAGTTTTTACCTCT336FANCC_ex9FFANCC_ex9Rgtaaaacgacggccag ATACTGCTGAAGCTTATGGCACAcaggaaacagctatga TAACCTTTGTTGGGGCACTCATT400FANCC_ex10FFANCC_ex10Rgtaaaacgacggccag TATGAGGTTATTGGGAGCTTATTcaggaaacagctatga CTGTCTCCCTCATGCTGTAGATA382FANCC_ex11FFANCC_ex11Rgtaaaacgacggccag GAACCAGAAGTAAAGGGCGTCTCcaggaaacagctatga CTGACCTGCTCCAAGCCATCCGT416FANCC_ex12FFANCC_ex12Rgtaaaacgacggccag AAGTACAATTTAAGCCAACCGTTcaggaaacagctatga AGGTTGCCATGACATATGCCATC451FANCC_ex13FFANCC_ex13Rgtaaaacgacggccag CCTCTCTCAGGGGCCAGTGCTTAcaggaaacagctatga AGACCCTCGGACAGGTAACCCAC435FANCC_ex14FFANCC_ex14Rgtaaaacgacggccag ACTTGCTATGCTAATCACCTTGCcaggaaacagctatga AATGCGTGGCCACAGGTCATCAC437(c)FANCEPrimer nameSequence (5′ > 3′)Product length (bp)FANCE_ex1FFANCE_ex1Rgtaaaacgacggccag CGCCTCCCTCCTTCCCTTTCcaggaaacagctatga CCCGCCTCCCATACCTGCTAA540FANCE_ex2aFFANCE_ex2aRgtaaaacgacggccag GCTCTGCCCAGTCTGCCTTGTGCcaggaaacagctatga CTCTGAGTCCTTTCTGCGTTTCC469FANCE_ex2bFFANCE_ex2bRgtaaaacgacggccag GCCAGAGACAGCTCCAAAGTCTAcaggaaacagctatga CAGCCTTCCCCATGGATAAAGCC479FANCE_ex3FFANCE_ex3Rgtaaaacgacggccag GCCTCTTGACTTTCTTGAATCATcaggaaacagctatga ACTGTCCTCAGACCTTTACTCCA352FANCE_ex4FFANCE_ex4Rgtaaaacgacggccag TTGAACCAAGTGTAGACTTACCAcaggaaacagctatga GGGAAGGAACCAAGGGCTAAAAG436FANCE_ex5FFANCE_ex5Rgtaaaacgacggccag GTATCTTTTAGCCCTTGGTTCCTcaggaaacagctatga GAATCCCCTCTCTCAAGTACCAC431FANCE_ex6FFANCE_ex6Rgtaaaacgacggccag TTTCCTTTGTAACATGTATCATCcaggaaacagctatga AGCAGAAAGCAGGGAGGCGGTAA433FANCE_ex7FFANCE_ex7Rgtaaaacgacggccag ACAGGCTGGGCATTCTGTTACCGcaggaaacagctatga AGTGAGACACAAGGATCCCCTAA425FANCE_ex8FFANCE_ex8Rgtaaaacgacggccag TTGGAGCAGCAGATAGATACTCAcaggaaacagctatga AGAGGTGGAGCTGAAGTGACCAT380FANCE_ex9FFANCE_ex9Rgtaaaacgacggccag GTTACCTGCCCAGGGTCACCTAGcaggaaacagctatga CTGGCCAGCACTCAGGGTTTTAT388FANCE_ex10FFANCE_ex10Rgtaaaacgacggccag TGGCCTCCTCTCTCCTCAATAGAcaggaaacagctatga AACAGGGAGGCAGTTGCAATCTG369(d)FANCFPrimer nameSequence (5′ > 3′)Product length (bp)FANCF_ex1aFFANCF_ex1aRgtaaaacgacggccag TTTCGCGGATGTTCCAATCAGTAcaggaaacagctatga CTGCACCAGGTGGTAACGAGCTG449FANCF_ex1bFFANCF_ex1bRgtaaaacgacggccag AGTGGAGGCAAGAGGGCGGCTTTcaggaaacagctatga GCTATCACCTTCAGGAAGTTGTT456FANCF_ex1cFFANCF_ex1cRgtaaaacgacggccag CCCAAATCTCCAGGAGGACTCTCcaggaaacagctatga TTTCTGAAGGTCATAGTGCAAAC444FANCF_ex1dFFANCF_ex1dRgtaaaacgacggccag GCTTTTGACTTTAGTGACTAGCCcaggaaacagctatga ATTTGGTGAGAACATTGTAATTT456(e)FANCGPrimer nameSequence (5′ > 3′)Product length (bp)FANCG_ex1FFANCG_ex1Rgtaaaacgacggccag AGCCTGGGCGGGTGGATTGGGACcaggaaacagctatga TCATTTCTGGCTCTTTGGTCAAG389FANCG_ex2FFANCG_ex2Rgtaaaacgacggccag CAGGCCAAGGTAACACGGTTGCTcaggaaacagctatga CCAGTCTCCTCTGTGCCTTAAAC460FANCG_ex3FFANCG_ex3Rgtaaaacgacggccag TATTGTAGCTGTTTTGGTTGGAGcaggaaacagctatga GGTGACAGATGTTGTTTATCCTC362FANCG_ex4FFANCG_ex4Rgtaaaacgacggccag GGAGATGGAGGATGAGGTGCTACcaggaaacagctatga CGACCACCAACCCAGCCGCCTGT411FANCG_ex5FFANCG_ex5Rgtaaaacgacggccag AGATGGAGATAGGAGAAGACGAGcaggaaacagctatga GCTTCATGAAGGCTGCTTAGTGC454FANCG_ex6FFANCG_ex6Rgtaaaacgacggccag CAGTTCCATGGGCTTCTTAGACCcaggaaacagctatga TCAGGGCTGCAACCAAGTACAAC393FANCG_ex7FFANCG_ex7Rgtaaaacgacggccag GCACTGGGGTCCTGTCACCGTAAcaggaaacagctatga ATAATCTTTGGGAGCCATACTTC418FANCG_ex8FFANCG_ex8Rgtaaaacgacggccag GCTTGTGATGGGGTGACTTGACTcaggaaacagctatga AGTTCAGGTCTAGAAGCAAGGTA438FANCG_ex9FFANCG_ex9Rgtaaaacgacggccag CCTCCTCAGGGCCCATGAACATCcaggaaacagctatga GCAGTGTCTTGAAAGGCATGAGC400FANCG_ex10FFANCG_ex10Rgtaaaacgacggccag CAGGACTCTGCATGGTACCAGcaggaaacagctatga CCAATCAGAAAATCATCCCTC460FANCG_ex11FFANCG_ex11Rgtaaaacgacggccag AGCTCCATGTTCACCTACTTACCcaggaaacagctatga CAGTGCCGCATCTGACTTACATC397FANCG_ex12FFANCG_ex12Rgtaaaacgacggccag AGGATTTGGGGTTTTGGTGACTGcaggaaacagctatga AACTCTTGGGAGCCCTGCATACA445FANCG_ex13FFANCG_ex13Rgtaaaacgacggccag CCGCTTCCATATGTGAGTGTAGGcaggaaacagctatgaC CACAATAGGTCCAAGGACTCTA340FANCG_ex14FFANCG_ex14Rgtaaaacgacggccag CCAAACTAAGGGGTCACATGAAGcaggaaacagctatga GATGGTGAAGCAGAAAGCCCTCC405(f)FANCBPrimer nameSequence (5′ > 3′)Product length (bp)FANCB_ex3AFFANCB_ex3ARgtaaaacgacggccag GATATGGTTATTTGAATTCTTAGCAcaggaaacagctatga GCCATCCTTCATCTCATAGCCTAGT721FANCB_ex3BFFANCB_ex3BRgtaaaacgacggccag ATTAACCTCCCTTACATTGTGATAGcaggaaacagctatga CAATAAGACTCCAGAATGAACTCTA811FANCB_ex4FFANCB_ex4Rgtaaaacgacggccag TTTACAAATGACAACTACATGAcaggaaacagctatga TTAAGTATAAAACCACCAATAT391FANCB_ex5FFANCB_ex5Rgtaaaacgacggccag ACTGCATCTGGCCTATAGTTcaggaaacagctatga AATACCATTTTTACCCAAGC411FANCB_ex6FFANCB_ex6Rgtaaaacgacggccag GTATTTCCTGAATTATTGGTATGTCcaggaaacagctatga CATAAAAGTCCACCATTATAACCTC395FANCB_ex7FFANCB_ex7Rgtaaaacgacggccag TGTTTGGGCCATAAGCCCTAcaggaaacagctatga  TTCTGGAGCATCAAGACAGT355FANCB_ex8FFANCB_ex8Rgtaaaacgacggccag GTTGTTTGTATGACATTTAATCATCcaggaaacagctatga ATCATTAAACTCTGCCCATTATCAG636FANCB_ex9FFANCB_ex9Rgtaaaacgacggccag AGGTAATTTTGTTGGCACTTcaggaaacagctatga ATGCGTTCATTCATGCTAGG531FANCB_ex10FFANCB_ex10Rgtaaaacgacggccag AATTGGTTCTGTTTATCATTATGGTcaggaaacagctatga CTACTACAGTAAGCCTCGGTGTTTA686PCR conditions:PCR was performed in Applied Biosystems PE9700 system using 96-well plates. PCR reactions (final volume 25μl) contained 0.5 units Platinum Taq polymerase (Invitrogen), 1,5 mM MgCl2, 0.2 mM NTPs (Invitrogen), and 10 pmol primer.For the large majority of amplicons, standard PCR conditions were used: preheat 95°C, 5 min, denaturation 95°C, 30 sec, annealing 60°C, 30 sec., elongation 72°C, 1 min, number of cycles: 33.Fragments with a different annealing temperature wereFANCA exons 5, 7, 13, 21, 26, 31, and 38, FANCC exon 7, FANCF fragment 1d and FANCE exon 1 : 55°C; FANCA exon  1 : 64°C. For FANCE exon 1 the PCR mix was supplemented with 10% DMSO.ForFANCB different PCR conditions were used: preheat 95°C, 5 min, denaturation 95°C, 1 min, annealing 50°C, 1 min., elongation 72°C, 1 min., number of cycles 30. For FANCB exon 7 and 9 the annealing temperature was 55°C. For sequencing of exon 7 forward, a special sequencing primer was used: 5′-TTTTTAGAAGGAATGTCTTG-3′.FA gene specific part of the primer is indicated in capitals. Primers are extended with M13 sequence (indicated in normal letter type), which is used for the sequencing reaction.After screeningFANCA, -C, -E, -F, -G, and –B, a molecular diagnosis is obtained for ~85% of the patients [34]. In our cohort of 54 patients, referred to our diagnostic service since 2008, mutations were detected in 45 patients (83%). FANCA mutations were found in 31 of the patients (57%), FANCC mutations in 6 patients (11%), and FANCG mutations in 5 patients (9%). FANCB, FANCE, and FANCF mutations were found in single families (Table 3). In the small group of patients without mutations no complementation analysis or FANCD2 western blotting was performed. Therefore, we do not know if we missed FANCA, -C, -E, -F, -G, and -B mutations in these patients or that these patients have mutations in other FA genes. Table 3 does not include prenatal cases, because prenatal testing is only offered in couples in which the FA-causing mutations are already established. Testing was offered as a diagnostic service for which a fee was charged.For the patients negative forFANCA, -C, -E, -F, -G, and -B mutations, next generation sequencing can be used to analyze all other FA genes. If this technique is not available, further analysis will depend on the availability of growing cells from the proband. In that case a western blot should reveal whether both FANCD2 isoforms are present at normal levels.(1)
If both FANCD2 bands are absent or very weak,FANCD2is sequenced. Because of the presence of FANCD2 pseudogene sequences in the genome, this testing must be performed on cDNA or gDNA using specially designed primers [26].(2)
If only the short isoform of FANCD2 is present,FANCL and FANCM are sequenced. If no mutations are found, the patient may be mutated in FANCI or in another unidentified FA gene acting upstream of FANCD2.(3)
If both isoforms are present, and if the clinical phenotype is compatible with FA-D1 or FA-N,BRCA2/FANCD1 and PALB2/FANCN are screened by MLPA and DNA sequencing.(4)
If negative,BRIP1/FANCJ, PALB2/FANCN, RAD51C/FANCO, and SLX4/FANCP are sequenced.(5)
If negative again, the patient should be screened for mutations inNBS1, ESCO2 and DDX11 to test for Nijmegen breakage syndrome, Roberts syndrome and Warsaw Breakage syndrome, respectively [47, 48]. The latter two syndromes can also be excluded by analyzing metaphase spreads for sister chromatid cohesion defects. If again negative, the patient is likely to be mutated in a novel FA gene acting downstream of FANCD2 ubiquitination.


## 2.2.1. Hints from Ethnic Background or Phenotype

Information on the ethnic background of the proband may provide a clue for a specific pathogenic mutation that most likely causes the disease, such as c.711 + 4A > T (IVS4 + 4A > T) inFANCC, a mutation present in homozygous state in 80% of all FA cases of Ashkenazi Jewish ancestry, and c.295C > T in FANCA, which was present homozygously in all 40 FA cases of Spanish Gypsy ancestry so far investigated. More examples of recurrent mutations are shown in Table 3. The distinct clinical phenotype of D1 and N patients (severely affected, often combined with leukemia or solid tumors below the age of 5 years) may provide a clue to favor BRCA2/FANCD1and PALB2/FANCN as the first gene to be screened [40–44]. This is especially worthwhile if confirmed by the cellular phenotype: in contrast to cells from all other known FA subtypes, cells from D1, N and O patients are unable to form RAD51 foci upon exposure to X rays or MMC [43–45].Table 3
Mutations detected in a cohort of 54 patients by screeningFANCA, FANCC, FANCE, FANCF and FANCG.
Allele 1Allele 2Country of origin1GeneDNA changeEffectNumber of database entriesDNA changeEffectNumber of database entries1ESFANCAex16_17deldel12xc.1115_1118delp.Val372fs62x2PTFANCAc.718C>Tp.Gln240X2xc.2870G>AW957X1x3NLFANCAex15deldel3xex15deldel3x4NLFANCAc.3788_3790delp.Phe1263del215xc.3788_3790delp.Phe1263del215x5CAFANCAc.718C>TpGlnx240X2xc.1085T>Cp.Leu362Pronovel6PTFANCAc.3788_3790delp.Phe1263del215xc.4130C>Gp.Ser1377X1x7IEFANCAc.2812_2830dupp.Asp944fs3xc.2812_2830dupp.Asp944fs3x8AUFANCAc.2303T>Cp.Leu768Pro5xc.2303T>Cp.Leu768Pro5x9NLFANCAc.862G>Tp.Glu288X1xc.862G>Tp.Glu288X1x10NLFANCAex11_33deldel1xc.2121delCp.Asn707fsnovel11DKFANCAex1_8deldel1xc.3788_3790delp.Phe1263del215x12UKFANCAc.337_338delp.Ala114fs1xc.3349A>Gp.Arg1117Gly2x13UKFANCAc.3568C>Tp.Gln1190Xnovelc.3568C>Tp.Gln1190Xnovel14NLFANCAc.487delCp.Arg163fs1xc.2851C>Tp.Arg951Trp11x15SEFANCAc.88delGp.Val30fsnovelc.100A>Tp.Lys34X2x16NLFANCAc.862G>Tp.Glu288X9xc.1771C>Tp.Arg591X9x17PTFANCAc.1709_1715+4delp.Glu570fsnovelc.3430C>Tp.Arg1144Trpnovel18NOFANCAc.100A>Tp.Lys34X2xc.1378C>Tp.Arg460Xnovel19PTFANCAex15_17deldel2xex15_17deldel2x20NLFANCAc.2982-192A>Gsplice2novelex7_31deldel21AUFANCAc.427-8_427-5delsplicenovelc.1771C>Tp.Arg591X9x22AUFANCAc.3491C>Tp.Pro1164Leunovelc.3491C>Tp.Pro1164Leunovel23CAFANCAex4_29deldelnovelex31deldel6x24NLFANCAc.3391A>Gp.Thr1131Ala15xc.3391A>Gp.Thr1131Ala15x25GRFANCAc.2T>Cp.Met1?1xc.3788_3790delp.Phe1263del215x26IEFANCAc.851dupp.Val285fsnovelc.2534T>Cp.Leu845Pro4x27NLFANCAc.2852G>Ap.Arg951Gln6xc.3624C>Tp.= (splice)2x28AUFANCAc.331_334dupp.Leu112fsnovelex22_29deldelnovel29NLFANCAc.862G>Tp.Glu288X9xc.3920delAp.Gln1307fs2x30IRFANCAex21deldelnovelex21deldelnovel31SEFANCAex1_12deldelnovelex22_29deldelnovel32NLFANCBc.755_767delp.Leu252fsnovel———33NLFANCCc.67delGp.Asp23fs50xc.553C>Tp.Arg185X14x34NLFANCCc.67delGp.Asp23fs50xc.67delGp.Asp23fs50x35CAFANCCc.67delGp.Asp23fs50xc.553C>Tp.Arg185X14x36NLFANCCc.67delGp.Asp23fs50xc.1155-1G>Csplicenovel37NLFANCCc.67delGp.Asp23fs50xc.67delGp.Asp23fs50x38NLFANCCc.67delGp.Asp23fs50xc.467delCp.Ser156fsnovel39PTFANCEc.1111C>Tp.Arg371Trp6xc.1111C>Tp.Arg371Trp6x40UKFANCFc.496C>Tp.Gln166X4xc.496C>Tp.Gln166X4x41UKFANCGc.307+2delTsplicenovelc.307+2delTsplicenovel42UKFANCGc.1471_1473delinsGp.Lys491fsnovelc.1471_1473delinsGp.Lys491fsnovel43NLFANCGc.65G>Cp.Arg22Pro6xc.65G>C;p.Arg22Pro6x44IRFANCGc.307+1G>Csplice21xc.307+1G>Csplice21x45NLFANCGc.85-1G>Asplicenovelc.85-1G>Asplicenovel1Country of origins: AU: Australia; CA: Canada; DK: Denmark; ES: Spain; GR: Greece; IE: Ireland; IR: Iran; NL: Netherlands; PT: Portugal; SE: Sweden; UK: United KingdomNumber of database entries refers to the FA database at:http://www.rockefeller.edu/fanconi/.The pathogenic state of novel missense mutations is based uponin silico prediction algorithms (SIFT, POLYPHEN2, Align GVGD), the presence of a second clearly pathogenic mutation in the same gene and segregation in the family.2Effect c.2982-192A>G: by studying cDNA it was shown that the mutation created a new splice donor site resulting in an aberrant mRNA.


## 2.2.2. No Clues Available

(1)
In the absence of any clue to the disease gene, mutation screening starts with a search for deletions inFANCA, as this type of mutation accounts for 40% of all mutant FANCA alleles. The quantitative multiplex ligation-dependent probe amplification (MLPA) method [46] is used for this initial screen, which identifies FANCA as the most likely disease gene in 1 out of 4 patients by the detection of a—usually hemizygous-deletion. In parallel, the FANCA gene is completely sequenced. The combination of these two approaches identifies 60–70% of all FA patients as FA-A.(2)
Next,FANCC, -E, -F, and -G are screened by DNA sequencing.(3)
Only if the proband is a male,FANCB is screened by MLPA and DNA sequencing,In Table4, optimized conditions are provided for the PCR amplification of FANCA, -C, -E, -F, -G, and -B. Most PCRs can be performed under standard conditions. The PCR primers have M13 extensions which allow sequencing of all fragments with universal sequencing primers. MLPA was performed according to the instructions of the supplier. Detailed information about the sequences of the MLPA probes is available from the website of the supplier (http://www.mlpa.com). In a well-equipped laboratory with sufficient dedicated personal, testing of FANCA, -C, -E, -F, -G and -B can be completed within 1-2 weeks.Table 4
Primers and conditions for PCR on genomic DNA of the coding sequence plus intron/exon boundaries ofFANCA, FANCC, FANCE, FANCF, FANCG,andFANCB.
(a)FANCAPrimer nameSequence (5′ > 3′)Product length (bp)FANCA_ex1Fgtaaaacgacggccag GCGCCTCCCCCAGGACCAACA362FANCA_ex1Rcaggaaacagctatga AGGCTCTGGCGGGAAGGGATCGGFANCA_ex2Fgtaaaacgacggccag CTCTTCGGGAGGGTGTCGCTGGT328FANCA_ex2Rcaggaaacagctatga CTCTTCGGGAGGGTGTCGCTGGTFANCA_ex3Fgtaaaacgacggccag GCCTGGCCTGGAGCTTGAAT392FANCA_ex3Rcaggaaacagctatga CGCAGGTTGAATCAGACGCTGTTFANCA_ex4Fgtaaaacgacggccag TAAGGCATTTTAAACAGCAAGTC430FANCA_ex4Rcaggaaacagctatga TGCCAATAAATACTGAGCAAACTFANCA_ex5Fgtaaaacgacggccag AGTATTGTTTCAGGTAATTTGTT356FANCA_ex5Rcaggaaacagctatga TGAAGGTACTTCTTTCCAATCCAFANCA_ex6Fgtaaaacgacggccag AGATGTGTTTCAGGCTCTAAGTT402FANCA_ex6Rcaggaaacagctatga GCAATGCAATCTAGTCTAGTACAFANCA_ex7Fgtaaaacgacggccag TGGGATTTAGTTGAGCCTTACGTCTGC421FANCA_ex7RcaggaaacagctatgaAAGGTGAATGGAAACACTTAAACTCATGTCAFANCA_ex8Fgtaaaacgacggccag GTGGTCAGGTGAGCAGTAACTTC401FANCA_ex8Rcaggaaacagctatga TAAATAGGTACAAACAGCACGTTFANCA_ex9Fgtaaaacgacggccag TTCTCTTGTGTGATGCAGGTATC332FANCA_ex9Rcaggaaacagctatga TGACCCACAGATTCATGAGGTATFANCA_ex10Fgtaaaacgacggccag TTTTGATTAAGGCCTACAGATTG406FANCA_ex10Rcaggaaacagctatga CCTCCTCCTCACGCACGTTATCGFANCA_ex11Fgtaaaacgacggccag TTTCAAGTCTGTGGTTATAGTGG410FANCA_ex11Rcaggaaacagctatga AGACGTAAAAGAGGTCCTAGAATFANCA_ex12Fgtaaaacgacggccag CTGTGGGGCTGGTCCTTAACAAA236FANCA_ex12Rcaggaaacagctatga AGGCAGCATGACAAGTACTAGGCFANCA_ex13Fgtaaaacgacggccag ACATTGGTTTGCTTGGATATTGA377FANCA_ex13Rcaggaaacagctatga CTGACAAAGAATGTTCCATCGACFANCA_ex14Fgtaaaacgacggccag TGCTGTAATTGCTGTGTAGTCTT411FANCA_ex14Rcaggaaacagctatga ACTCACATGACAGAGAATCAGGTFANCA_ex15Fgtaaaacgacggccag ACTACAGCAGCCGCCCGGACACT430FANCA_ex15Rcaggaaacagctatga GCAGATCTGCAGGAGGCTCTTGGFANCA_ex16Fgtaaaacgacggccag TCCCAGGCAGTTCCCAGACTAAC312FANCA_ex16Rcaggaaacagctatga AGCTGATGACAAATCCTCGTAGAFANCA_ex17Fgtaaaacgacggccag ACCGCTCCCTCCTCACAGACTAC334FANCA_ex17Rcaggaaacagctatga AAGGCTGAAAAACTCAACTCAAGFANCA_ex18Fgtaaaacgacggccag GCGCACAGCATGTGGGCCTTTAC397FANCA_ex18Rcaggaaacagctatga GCAGCTGCTAGAGGCCTTTTCGGFANCA_ex19Fgtaaaacgacggccag GTGCACAAGAAGACTTCATAATG284FANCA_ex19Rcaggaaacagctatga AGTCCTTGCTTTCTACACAACTGFANCA_ex20Fgtaaaacgacggccag CTTCTCTGTGTTGCAGCATATTC298FANCA_ex20Rcaggaaacagctatga AGAAGAAACCTGGAAGTAGTCATFANCA_ex21Fgtaaaacgacggccag ATAATAGATTTGGGGATTGTAAT255FANCA_ex21Rcaggaaacagctatga CAACAGACACTCAAGGTTAGGAAFANCA_ex22Fgtaaaacgacggccag TGCAGTGAAGAGTCCTGTTGAGT305FANCA_ex22Rcaggaaacagctatga ACACACCAGCCTGATGTCACTATFANCA_ex23Fgtaaaacgacggccag CAGTCAGCAGGATCCGTGGAATC416FANCA_ex23Rcaggaaacagctatga GGCCCTGGAACATCTGATACGACFANCA_ex24Fgtaaaacgacggccag CCTTCCTGCTGCTCCCGTCC229FANCA_ex24Rcaggaaacagctatga CAGACTTGGCCCAGCAAGAGFANCA_ex25Fgtaaaacgacggccag CCGCTGGTGGTTGGATTAGCTGT296FANCA_ex25Rcaggaaacagctatga TTTCCAGGGCACTGAAGACGAATFANCA_ex26Fgtaaaacgacggccag AGCTTGGAAGAGGGCAGTCTGCT347FANCA_ex26Rcaggaaacagctatga CTCTTCTAATTTTATCAAACGAGFANCA_ex27Fgtaaaacgacggccag AGACTGTCTCACAACAAACGAAC356FANCA_ex27Rcaggaaacagctatga CGGTCCGAAAGCTGCGTAAACFANCA_ex28Fgtaaaacgacggccag GTTGATGGTCTGTTTCCACCTGA401FANCA_ex28Rcaggaaacagctatga GAAGGAACGGTCACCTACGTGCTFANCA_ex29Fgtaaaacgacggccag GACATGGAGGACTGCGTATGAGA411FANCA_ex29Rcaggaaacagctatga GTGGCTGTGATGACTGGAACGTGFANCA_ex30Fgtaaaacgacggccag CCCGAGCCGCCAGTCTCAACCCA411FANCA_ex30Rcaggaaacagctatga AAAGGCAGACCCACCCTAAGCTAFANCA_ex31Fgtaaaacgacggccag GATAAGCCTCCTTGGTCATGGTA406FANCA_ex31Rcaggaaacagctatga TGGCAATAAATATCTTAATAGCAFANCA_ex32Fgtaaaacgacggccag TTCCTGTGCCAGCATACTGCTCT359FANCA_ex32Rcaggaaacagctatga GGGTGGGGACACACAGACAAGTAFANCA_ex33Fgtaaaacgacggccag TGGGTTTCAGGGTGGTGGTTGCT356FANCA_ex33Rcaggaaacagctatga GAACCCTTTCCTCAGTAATTCACFANCA_ex34Fgtaaaacgacggccag CGCCCAGGGAAGCCGTTAAGTTT333FANCA_ex34Rcaggaaacagctatga GCGTTCTGAGAAGGCCACGAGAGFANCA_ex35Fgtaaaacgacggccag TTCCTTCACTCTACTAGTTGTGG311FANCA_ex35Rcaggaaacagctatga TGAGATGGTAACACCCGTGATGGFANCA_ex36Fgtaaaacgacggccag CCATCTCAGCCACCCTCATCTGT350FANCA_ex36Rcaggaaacagctatga AGGCGCCCACCACCACGAGAACTFANCA_ex37Fgtaaaacgacggccag GACTTGGTTTCTATGGCGTGGTT310FANCA_ex37Rcaggaaacagctatga CCCAGAGAAATAGCACTGATTGAFANCA_ex38Fgtaaaacgacggccag GTTTTCTAAGATCCACTTAAAGG362FANCA_ex38Rcaggaaacagctatga CTCACTCACACTTCCGCAAACACFANCA_ex39Fgtaaaacgacggccag CTGTCCAGAGGCCCAGTATTACC387FANCA_ex39Rcaggaaacagctatga AGGAGGGCTCGTTCTTAACCATTFANCA_ex40Fgtaaaacgacggccag GGTGTCCCCAGCACTGATAATAG353FANCA_ex40Rcaggaaacagctatga AGACATAGTGACAAATGGCTACAFANCA_ex41Fgtaaaacgacggccag CCCTTGGCATCACCTGCTACCTT403FANCA_ex41Rcaggaaacagctatga AACAGGCAAACTCACAGGTTAGAFANCA_ex42Fgtaaaacgacggccag ACCAGCCCTGTTTCTGTATGTCT248FANCA_ex42Rcaggaaacagctatga ACATGGCCCAGGCAGCTGTCAATFANCA_ex43Fgtaaaacgacggccag TGTGGGGGACATGAGAATTGACA378FANCA_ex43Rcaggaaacagctatga GTAATCCACTTTTTAGTGCAACAFANCAIVS10Fgtaaaacgacggccag TTTACATGTGCATCAGTTAGCTT184FANCAIVS10Rcaggaaacagctatga CATGAAGACACAGAAAAAGTAGGT(b)FANCCPrimer nameSequence (5′ > 3′)Product length (bp)FANCC_ex1FFANCC_ex1Rgtaaaacgacggccag ACCATTTCCTTCAGTGCTGGACAcaggaaacagctatga CCATCGGCACTTCAGTCAATACC378FANCC_ex2FFANCC_ex2Rgtaaaacgacggccag CTAAACAAGAAGCATTCACGTTCcaggaaacagctatga GGAGAAAGGTTCATAATGTAAGC303FANCC_ex3FFANCC_ex3Rgtaaaacgacggccag TCAGCAGAAAGAGAATGTGCAAAcaggaaacagctatga AACATCATAGAACTGGATTCCAC405FANCC_ex4FFANCC_ex4Rgtaaaacgacggccag TGTACATAAAAGGCACTTGCATTcaggaaacagctatga TCCCATCTCACATTTCTTCCGTA380FANCC_ex5FFANCC_ex5Rgtaaaacgacggccag AGAACTGATGTAATCCTGTTTGCcaggaaacagctatga TTACTGCTCTGTGAGAGTTGAGA367FANCC_ex6FFANCC_ex6Rgtaaaacgacggccag GTCTTTGACCTTTTTAGCATGAAcaggaaacagctatga AACGTTTGGACACTGCTGTCGTA387FANCC_ex7FFANCC_ex7Rgtaaaacgacggccag ATTAGTGATTGCATTTTGAACTTcaggaaacagctatga CAAAAATAAAATGTAAATACACG422FANCC_ex8FFANCC_ex8Rgtaaaacgacggccag CTCCTTTGGCTGATAATAGCAAGcaggaaacagctatga CTGATTTTTGAGTTTTTACCTCT336FANCC_ex9FFANCC_ex9Rgtaaaacgacggccag ATACTGCTGAAGCTTATGGCACAcaggaaacagctatga TAACCTTTGTTGGGGCACTCATT400FANCC_ex10FFANCC_ex10Rgtaaaacgacggccag TATGAGGTTATTGGGAGCTTATTcaggaaacagctatga CTGTCTCCCTCATGCTGTAGATA382FANCC_ex11FFANCC_ex11Rgtaaaacgacggccag GAACCAGAAGTAAAGGGCGTCTCcaggaaacagctatga CTGACCTGCTCCAAGCCATCCGT416FANCC_ex12FFANCC_ex12Rgtaaaacgacggccag AAGTACAATTTAAGCCAACCGTTcaggaaacagctatga AGGTTGCCATGACATATGCCATC451FANCC_ex13FFANCC_ex13Rgtaaaacgacggccag CCTCTCTCAGGGGCCAGTGCTTAcaggaaacagctatga AGACCCTCGGACAGGTAACCCAC435FANCC_ex14FFANCC_ex14Rgtaaaacgacggccag ACTTGCTATGCTAATCACCTTGCcaggaaacagctatga AATGCGTGGCCACAGGTCATCAC437(c)FANCEPrimer nameSequence (5′ > 3′)Product length (bp)FANCE_ex1FFANCE_ex1Rgtaaaacgacggccag CGCCTCCCTCCTTCCCTTTCcaggaaacagctatga CCCGCCTCCCATACCTGCTAA540FANCE_ex2aFFANCE_ex2aRgtaaaacgacggccag GCTCTGCCCAGTCTGCCTTGTGCcaggaaacagctatga CTCTGAGTCCTTTCTGCGTTTCC469FANCE_ex2bFFANCE_ex2bRgtaaaacgacggccag GCCAGAGACAGCTCCAAAGTCTAcaggaaacagctatga CAGCCTTCCCCATGGATAAAGCC479FANCE_ex3FFANCE_ex3Rgtaaaacgacggccag GCCTCTTGACTTTCTTGAATCATcaggaaacagctatga ACTGTCCTCAGACCTTTACTCCA352FANCE_ex4FFANCE_ex4Rgtaaaacgacggccag TTGAACCAAGTGTAGACTTACCAcaggaaacagctatga GGGAAGGAACCAAGGGCTAAAAG436FANCE_ex5FFANCE_ex5Rgtaaaacgacggccag GTATCTTTTAGCCCTTGGTTCCTcaggaaacagctatga GAATCCCCTCTCTCAAGTACCAC431FANCE_ex6FFANCE_ex6Rgtaaaacgacggccag TTTCCTTTGTAACATGTATCATCcaggaaacagctatga AGCAGAAAGCAGGGAGGCGGTAA433FANCE_ex7FFANCE_ex7Rgtaaaacgacggccag ACAGGCTGGGCATTCTGTTACCGcaggaaacagctatga AGTGAGACACAAGGATCCCCTAA425FANCE_ex8FFANCE_ex8Rgtaaaacgacggccag TTGGAGCAGCAGATAGATACTCAcaggaaacagctatga AGAGGTGGAGCTGAAGTGACCAT380FANCE_ex9FFANCE_ex9Rgtaaaacgacggccag GTTACCTGCCCAGGGTCACCTAGcaggaaacagctatga CTGGCCAGCACTCAGGGTTTTAT388FANCE_ex10FFANCE_ex10Rgtaaaacgacggccag TGGCCTCCTCTCTCCTCAATAGAcaggaaacagctatga AACAGGGAGGCAGTTGCAATCTG369(d)FANCFPrimer nameSequence (5′ > 3′)Product length (bp)FANCF_ex1aFFANCF_ex1aRgtaaaacgacggccag TTTCGCGGATGTTCCAATCAGTAcaggaaacagctatga CTGCACCAGGTGGTAACGAGCTG449FANCF_ex1bFFANCF_ex1bRgtaaaacgacggccag AGTGGAGGCAAGAGGGCGGCTTTcaggaaacagctatga GCTATCACCTTCAGGAAGTTGTT456FANCF_ex1cFFANCF_ex1cRgtaaaacgacggccag CCCAAATCTCCAGGAGGACTCTCcaggaaacagctatga TTTCTGAAGGTCATAGTGCAAAC444FANCF_ex1dFFANCF_ex1dRgtaaaacgacggccag GCTTTTGACTTTAGTGACTAGCCcaggaaacagctatga ATTTGGTGAGAACATTGTAATTT456(e)FANCGPrimer nameSequence (5′ > 3′)Product length (bp)FANCG_ex1FFANCG_ex1Rgtaaaacgacggccag AGCCTGGGCGGGTGGATTGGGACcaggaaacagctatga TCATTTCTGGCTCTTTGGTCAAG389FANCG_ex2FFANCG_ex2Rgtaaaacgacggccag CAGGCCAAGGTAACACGGTTGCTcaggaaacagctatga CCAGTCTCCTCTGTGCCTTAAAC460FANCG_ex3FFANCG_ex3Rgtaaaacgacggccag TATTGTAGCTGTTTTGGTTGGAGcaggaaacagctatga GGTGACAGATGTTGTTTATCCTC362FANCG_ex4FFANCG_ex4Rgtaaaacgacggccag GGAGATGGAGGATGAGGTGCTACcaggaaacagctatga CGACCACCAACCCAGCCGCCTGT411FANCG_ex5FFANCG_ex5Rgtaaaacgacggccag AGATGGAGATAGGAGAAGACGAGcaggaaacagctatga GCTTCATGAAGGCTGCTTAGTGC454FANCG_ex6FFANCG_ex6Rgtaaaacgacggccag CAGTTCCATGGGCTTCTTAGACCcaggaaacagctatga TCAGGGCTGCAACCAAGTACAAC393FANCG_ex7FFANCG_ex7Rgtaaaacgacggccag GCACTGGGGTCCTGTCACCGTAAcaggaaacagctatga ATAATCTTTGGGAGCCATACTTC418FANCG_ex8FFANCG_ex8Rgtaaaacgacggccag GCTTGTGATGGGGTGACTTGACTcaggaaacagctatga AGTTCAGGTCTAGAAGCAAGGTA438FANCG_ex9FFANCG_ex9Rgtaaaacgacggccag CCTCCTCAGGGCCCATGAACATCcaggaaacagctatga GCAGTGTCTTGAAAGGCATGAGC400FANCG_ex10FFANCG_ex10Rgtaaaacgacggccag CAGGACTCTGCATGGTACCAGcaggaaacagctatga CCAATCAGAAAATCATCCCTC460FANCG_ex11FFANCG_ex11Rgtaaaacgacggccag AGCTCCATGTTCACCTACTTACCcaggaaacagctatga CAGTGCCGCATCTGACTTACATC397FANCG_ex12FFANCG_ex12Rgtaaaacgacggccag AGGATTTGGGGTTTTGGTGACTGcaggaaacagctatga AACTCTTGGGAGCCCTGCATACA445FANCG_ex13FFANCG_ex13Rgtaaaacgacggccag CCGCTTCCATATGTGAGTGTAGGcaggaaacagctatgaC CACAATAGGTCCAAGGACTCTA340FANCG_ex14FFANCG_ex14Rgtaaaacgacggccag CCAAACTAAGGGGTCACATGAAGcaggaaacagctatga GATGGTGAAGCAGAAAGCCCTCC405(f)FANCBPrimer nameSequence (5′ > 3′)Product length (bp)FANCB_ex3AFFANCB_ex3ARgtaaaacgacggccag GATATGGTTATTTGAATTCTTAGCAcaggaaacagctatga GCCATCCTTCATCTCATAGCCTAGT721FANCB_ex3BFFANCB_ex3BRgtaaaacgacggccag ATTAACCTCCCTTACATTGTGATAGcaggaaacagctatga CAATAAGACTCCAGAATGAACTCTA811FANCB_ex4FFANCB_ex4Rgtaaaacgacggccag TTTACAAATGACAACTACATGAcaggaaacagctatga TTAAGTATAAAACCACCAATAT391FANCB_ex5FFANCB_ex5Rgtaaaacgacggccag ACTGCATCTGGCCTATAGTTcaggaaacagctatga AATACCATTTTTACCCAAGC411FANCB_ex6FFANCB_ex6Rgtaaaacgacggccag GTATTTCCTGAATTATTGGTATGTCcaggaaacagctatga CATAAAAGTCCACCATTATAACCTC395FANCB_ex7FFANCB_ex7Rgtaaaacgacggccag TGTTTGGGCCATAAGCCCTAcaggaaacagctatga  TTCTGGAGCATCAAGACAGT355FANCB_ex8FFANCB_ex8Rgtaaaacgacggccag GTTGTTTGTATGACATTTAATCATCcaggaaacagctatga ATCATTAAACTCTGCCCATTATCAG636FANCB_ex9FFANCB_ex9Rgtaaaacgacggccag AGGTAATTTTGTTGGCACTTcaggaaacagctatga ATGCGTTCATTCATGCTAGG531FANCB_ex10FFANCB_ex10Rgtaaaacgacggccag AATTGGTTCTGTTTATCATTATGGTcaggaaacagctatga CTACTACAGTAAGCCTCGGTGTTTA686PCR conditions:PCR was performed in Applied Biosystems PE9700 system using 96-well plates. PCR reactions (final volume 25μl) contained 0.5 units Platinum Taq polymerase (Invitrogen), 1,5 mM MgCl2, 0.2 mM NTPs (Invitrogen), and 10 pmol primer.For the large majority of amplicons, standard PCR conditions were used: preheat 95°C, 5 min, denaturation 95°C, 30 sec, annealing 60°C, 30 sec., elongation 72°C, 1 min, number of cycles: 33.Fragments with a different annealing temperature wereFANCA exons 5, 7, 13, 21, 26, 31, and 38, FANCC exon 7, FANCF fragment 1d and FANCE exon 1 : 55°C; FANCA exon  1 : 64°C. For FANCE exon 1 the PCR mix was supplemented with 10% DMSO.ForFANCB different PCR conditions were used: preheat 95°C, 5 min, denaturation 95°C, 1 min, annealing 50°C, 1 min., elongation 72°C, 1 min., number of cycles 30. For FANCB exon 7 and 9 the annealing temperature was 55°C. For sequencing of exon 7 forward, a special sequencing primer was used: 5′-TTTTTAGAAGGAATGTCTTG-3′.FA gene specific part of the primer is indicated in capitals. Primers are extended with M13 sequence (indicated in normal letter type), which is used for the sequencing reaction.After screeningFANCA, -C, -E, -F, -G, and –B, a molecular diagnosis is obtained for ~85% of the patients [34]. In our cohort of 54 patients, referred to our diagnostic service since 2008, mutations were detected in 45 patients (83%). FANCA mutations were found in 31 of the patients (57%), FANCC mutations in 6 patients (11%), and FANCG mutations in 5 patients (9%). FANCB, FANCE, and FANCF mutations were found in single families (Table 3). In the small group of patients without mutations no complementation analysis or FANCD2 western blotting was performed. Therefore, we do not know if we missed FANCA, -C, -E, -F, -G, and -B mutations in these patients or that these patients have mutations in other FA genes. Table 3 does not include prenatal cases, because prenatal testing is only offered in couples in which the FA-causing mutations are already established. Testing was offered as a diagnostic service for which a fee was charged.For the patients negative forFANCA, -C, -E, -F, -G, and -B mutations, next generation sequencing can be used to analyze all other FA genes. If this technique is not available, further analysis will depend on the availability of growing cells from the proband. In that case a western blot should reveal whether both FANCD2 isoforms are present at normal levels.(1)
If both FANCD2 bands are absent or very weak,FANCD2is sequenced. Because of the presence of FANCD2 pseudogene sequences in the genome, this testing must be performed on cDNA or gDNA using specially designed primers [26].(2)
If only the short isoform of FANCD2 is present,FANCL and FANCM are sequenced. If no mutations are found, the patient may be mutated in FANCI or in another unidentified FA gene acting upstream of FANCD2.(3)
If both isoforms are present, and if the clinical phenotype is compatible with FA-D1 or FA-N,BRCA2/FANCD1 and PALB2/FANCN are screened by MLPA and DNA sequencing.(4)
If negative,BRIP1/FANCJ, PALB2/FANCN, RAD51C/FANCO, and SLX4/FANCP are sequenced.(5)
If negative again, the patient should be screened for mutations inNBS1, ESCO2 and DDX11 to test for Nijmegen breakage syndrome, Roberts syndrome and Warsaw Breakage syndrome, respectively [47, 48]. The latter two syndromes can also be excluded by analyzing metaphase spreads for sister chromatid cohesion defects. If again negative, the patient is likely to be mutated in a novel FA gene acting downstream of FANCD2 ubiquitination.


## 3. Notes

### 3.1. Mutation Screening in Mosaic Patients

If an available lymphoblastoid cell line from an FA patient is phenotypically normal due to genetic reversion at the disease locus, mutation screening is still possible in the reverted cell line, since at least one mutation will be present [49–51]. The second mutation may be identified through investigating the parents.


### 3.2. Unclassified Variants

Missense mutations orin-frame deletions or insertions should be judged using in silico prediction algorithms (SIFT, POLYPHEN2, Align GVGD). Alternatively, they can be tested for pathogenicity in a cellular transfection assay to check the ability of the variant gene product to complement the cellular FA defect in a deficient cell line (see e.g., [10, 35, 52]). Generally, these tests are only feasible in a setting where a diagnostic laboratory is equipped with a research laboratory with all necessary technology.


### 3.3. Functional Assignment to Genetic Subtypes

Retroviral constructs have been used to identify the FA subtype by functional complementation, as an intermediate step before a mutation screen is undertaken [36]. Although knowing the disease gene facilitates mutation screening, retroviral transduction has some drawbacks in comparison to direct mutation screening: (i) growing, MMC-sensitive cells either from a cell line or fresh blood sample are required, which are not always easy to obtain; (ii) overexpression of some FA proteins (e.g., FANCM and FANCP) may be toxic for cells; (iii) novel genetic subtypes that emerge after all known groups have been excluded and cannot be readily distinguished from false negatives, that is, transductions that for some unknown reason have failed to cause complementation; (iv) the method requires relatively advanced laboratory facilities and technology. However, functional assignment of complementation group can rapidly be provided by laboratories with capability for this type of analysis [37], which has greatly facilitated reliable genotyping for over 95% of FA patients for which viral constructs are available.


### 3.4. Genetic Counseling

All patients with a diagnosis of FA confirmed by mutation analysis should be referred for genetic counselling, together with their parents and siblings. Mutation testing should be performed in all sibs regardless of any clinical symptoms. A complete pedigree, including a cancer history anamnesis, should be prepared. Mutation carriers might be at increased cancer risk (see Section3.7) whose aspect should be included in the counseling (see Section 3.7).FA patients themselves usually have decreased fertility. Women usually have late menarche, irregular menses, and early menopause. However, pregnancies in women with FA have been described, and therefore women should be adequately informed about the risks for their offspring, which is mainly related to an increase in pregnancy-related complications [53].Sibs of the parents of an FA patient often request carrier screening to assess their risk of getting a child with FA. If a sib appears to be carrier, this risk is still minimal because of the very low carrier frequency in the population. In the US the carrier frequency has been estimated to be about 1 in 181 [54]. The risk of a proven carrier to get a child with FA is therefore about 1 in 724. However, in small communities or in consanguineous couples this risk is much higher, and mutation screening in spouses of proven carriers may be indicated.


### 3.5. Prenatal Diagnosis

Prenatal diagnosis of FA is relatively straightforward after the pathogenic mutations in a given family have been identified. Fetal cells can be obtained by chorionic villus sampling (CVS) during weeks 10–12 of the pregnancy or by amniocentesis, which is performed between weeks 14 and 16. However, CVS may be preferred as the diagnosis will be known at an earlier stage. If the mutation is not known, a chromosomal breakage test on fetal material may be performed [55], but this test may be considered less reliable than screening for mutations in the fetal material. Alternatively, flow cytometric testing of MMC sensitivity in amniotic cell cultures might be an option; however this technique is only available in a limited number of specialized laboratories [56]. Occasionally, FA may be suspected by fetal ultrasound imaging and confirmed by parental carrier testing when the family is not yet known to carry a risk for FA [57].


### 3.6. Genotype-Phenotype Correlation

FA is considered as one disease, and the question may be raised whether all fifteen genetic subtypes equally conform to the clinical FA phenotype. Genotype-phenotype correlation studies comparing the 3 most common groups A, C, and G indicated modest phenotypic differences, which were rather correlated with the relative severity of the mutations [23]. However, bias due to the ethnic distribution of the studied population is very well possible. Other studies reported significant differences between FA-A/G versus FA-C [58]. Cases in group FA-D1 (mutated in BRCA2) and FA-N (mutated in PALB2) present with a distinct, relatively severe, phenotype that is characterized by the development of leukemia at very young age (median 2.2 years) and by pediatric cancers such as nephroblastoma (Wilms tumor) or medulloblastoma [40–44]. The observations that one of the pathogenic mutations in BRCA2 in FA-D1 patients is hypomorphic and that mice with biallelic null alleles in Brca2 are embryonic lethals suggest that the BRCA2 protein serves a function that is essential for survival.Different mutations in the same gene may be associated with divergent phenotypes, as illustrated by the twoFANCC mutations, c.711+4A>T and c.67delG. The former (splice-site) mutation is associated with a relatively severe phenotype in Ashkenazi Jewish people [19] although the associated phenotype was reportedly less severe in patients of Japanese ancestry [20]. The carrier frequency for this mutation in the Ashkenazi population is relatively high (1 in 87), which has led to the recommendation of carrier detection to prevent disease [59]. In the Netherlands more than 50% of FA cases are homozygous for the FANCC frameshift mutation c.67delG. The phenotype associated with this mutation, like other exon 1 mutations, seems relatively mild, as these patients rarely have skeletal abnormalities and show a relatively late age of onset of their marrow failure [24]. Awareness of such genetically determined phenotypic differences may help in clinical decision making, including the counselling of patients and families.


### 3.7. Cancer Risk in Heterozygous Mutation Carriers

An important issue is whether FA mutation carriers are at increased risk to develop cancer or other types of disease. Overall, there is no increased risk for cancer among FA heterozygotes [60, 61]. However, the situation is different in some of the less prevalent FA subtypes. The FA-D1 subtype is caused by mutations in BRCA2 [62] which is a well-known breast and ovarian cancer predisposition gene [63]. In FA-D1 one of the mutations will be hypomorphic because biallelic “severe” mutations are supposed to be lethal [26]. Therefore, one of the parents of a FA-D1 patient will be a heterozygous carrier of a “severe” inactivating BRCA2mutation and may thus have an increased risk for breast cancer and other BRCA2-associated cancers. Whether the parent with the hypomorphic mutation is also at increased risk is unknown: in breast cancer families these hypomorphic mutations are considered as variants with unknown clinical significance. Two other genes involved in FA and related to breast or ovarian cancer predisposition are PALB2/FANCN [64, 65] and RAD51C/FANCO [66]. Although cancer patients have been identified with germ-line mutations in these genes, an accurate estimate of the relative cancer risk for mutation carriers is still lacking.Another special case is represented by femaleFANCB mutation carriers, who are supposed to consist of 50% FA-like cells due to silenced expression of the wild type FANCB allele by the random process of X inactivation that occurs during early embryonic development. Nevertheless, in the few female FANCB mutation carriers studied so far, inactivation appeared strongly skewed towards the mutated allele [67]. This suggests that FA cells have a poor chance to survive next to unaffected cells in the same tissue, and these FA cells may therefore not give an increased cancer risk. However, the data are scarce at present so that no firm conclusions can be drawn regarding the cancer risk of female FANCB mutation carriers [60].


## 3.1. Mutation Screening in Mosaic Patients

If an available lymphoblastoid cell line from an FA patient is phenotypically normal due to genetic reversion at the disease locus, mutation screening is still possible in the reverted cell line, since at least one mutation will be present [49–51]. The second mutation may be identified through investigating the parents.


## 3.2. Unclassified Variants

Missense mutations orin-frame deletions or insertions should be judged using in silico prediction algorithms (SIFT, POLYPHEN2, Align GVGD). Alternatively, they can be tested for pathogenicity in a cellular transfection assay to check the ability of the variant gene product to complement the cellular FA defect in a deficient cell line (see e.g., [10, 35, 52]). Generally, these tests are only feasible in a setting where a diagnostic laboratory is equipped with a research laboratory with all necessary technology.


## 3.3. Functional Assignment to Genetic Subtypes

Retroviral constructs have been used to identify the FA subtype by functional complementation, as an intermediate step before a mutation screen is undertaken [36]. Although knowing the disease gene facilitates mutation screening, retroviral transduction has some drawbacks in comparison to direct mutation screening: (i) growing, MMC-sensitive cells either from a cell line or fresh blood sample are required, which are not always easy to obtain; (ii) overexpression of some FA proteins (e.g., FANCM and FANCP) may be toxic for cells; (iii) novel genetic subtypes that emerge after all known groups have been excluded and cannot be readily distinguished from false negatives, that is, transductions that for some unknown reason have failed to cause complementation; (iv) the method requires relatively advanced laboratory facilities and technology. However, functional assignment of complementation group can rapidly be provided by laboratories with capability for this type of analysis [37], which has greatly facilitated reliable genotyping for over 95% of FA patients for which viral constructs are available.


## 3.4. Genetic Counseling

All patients with a diagnosis of FA confirmed by mutation analysis should be referred for genetic counselling, together with their parents and siblings. Mutation testing should be performed in all sibs regardless of any clinical symptoms. A complete pedigree, including a cancer history anamnesis, should be prepared. Mutation carriers might be at increased cancer risk (see Section3.7) whose aspect should be included in the counseling (see Section 3.7).FA patients themselves usually have decreased fertility. Women usually have late menarche, irregular menses, and early menopause. However, pregnancies in women with FA have been described, and therefore women should be adequately informed about the risks for their offspring, which is mainly related to an increase in pregnancy-related complications [53].Sibs of the parents of an FA patient often request carrier screening to assess their risk of getting a child with FA. If a sib appears to be carrier, this risk is still minimal because of the very low carrier frequency in the population. In the US the carrier frequency has been estimated to be about 1 in 181 [54]. The risk of a proven carrier to get a child with FA is therefore about 1 in 724. However, in small communities or in consanguineous couples this risk is much higher, and mutation screening in spouses of proven carriers may be indicated.


## 3.5. Prenatal Diagnosis

Prenatal diagnosis of FA is relatively straightforward after the pathogenic mutations in a given family have been identified. Fetal cells can be obtained by chorionic villus sampling (CVS) during weeks 10–12 of the pregnancy or by amniocentesis, which is performed between weeks 14 and 16. However, CVS may be preferred as the diagnosis will be known at an earlier stage. If the mutation is not known, a chromosomal breakage test on fetal material may be performed [55], but this test may be considered less reliable than screening for mutations in the fetal material. Alternatively, flow cytometric testing of MMC sensitivity in amniotic cell cultures might be an option; however this technique is only available in a limited number of specialized laboratories [56]. Occasionally, FA may be suspected by fetal ultrasound imaging and confirmed by parental carrier testing when the family is not yet known to carry a risk for FA [57].


## 3.6. Genotype-Phenotype Correlation

FA is considered as one disease, and the question may be raised whether all fifteen genetic subtypes equally conform to the clinical FA phenotype. Genotype-phenotype correlation studies comparing the 3 most common groups A, C, and G indicated modest phenotypic differences, which were rather correlated with the relative severity of the mutations [23]. However, bias due to the ethnic distribution of the studied population is very well possible. Other studies reported significant differences between FA-A/G versus FA-C [58]. Cases in group FA-D1 (mutated in BRCA2) and FA-N (mutated in PALB2) present with a distinct, relatively severe, phenotype that is characterized by the development of leukemia at very young age (median 2.2 years) and by pediatric cancers such as nephroblastoma (Wilms tumor) or medulloblastoma [40–44]. The observations that one of the pathogenic mutations in BRCA2 in FA-D1 patients is hypomorphic and that mice with biallelic null alleles in Brca2 are embryonic lethals suggest that the BRCA2 protein serves a function that is essential for survival.Different mutations in the same gene may be associated with divergent phenotypes, as illustrated by the twoFANCC mutations, c.711+4A>T and c.67delG. The former (splice-site) mutation is associated with a relatively severe phenotype in Ashkenazi Jewish people [19] although the associated phenotype was reportedly less severe in patients of Japanese ancestry [20]. The carrier frequency for this mutation in the Ashkenazi population is relatively high (1 in 87), which has led to the recommendation of carrier detection to prevent disease [59]. In the Netherlands more than 50% of FA cases are homozygous for the FANCC frameshift mutation c.67delG. The phenotype associated with this mutation, like other exon 1 mutations, seems relatively mild, as these patients rarely have skeletal abnormalities and show a relatively late age of onset of their marrow failure [24]. Awareness of such genetically determined phenotypic differences may help in clinical decision making, including the counselling of patients and families.


## 3.7. Cancer Risk in Heterozygous Mutation Carriers

An important issue is whether FA mutation carriers are at increased risk to develop cancer or other types of disease. Overall, there is no increased risk for cancer among FA heterozygotes [60, 61]. However, the situation is different in some of the less prevalent FA subtypes. The FA-D1 subtype is caused by mutations in BRCA2 [62] which is a well-known breast and ovarian cancer predisposition gene [63]. In FA-D1 one of the mutations will be hypomorphic because biallelic “severe” mutations are supposed to be lethal [26]. Therefore, one of the parents of a FA-D1 patient will be a heterozygous carrier of a “severe” inactivating BRCA2mutation and may thus have an increased risk for breast cancer and other BRCA2-associated cancers. Whether the parent with the hypomorphic mutation is also at increased risk is unknown: in breast cancer families these hypomorphic mutations are considered as variants with unknown clinical significance. Two other genes involved in FA and related to breast or ovarian cancer predisposition are PALB2/FANCN [64, 65] and RAD51C/FANCO [66]. Although cancer patients have been identified with germ-line mutations in these genes, an accurate estimate of the relative cancer risk for mutation carriers is still lacking.Another special case is represented by femaleFANCB mutation carriers, who are supposed to consist of 50% FA-like cells due to silenced expression of the wild type FANCB allele by the random process of X inactivation that occurs during early embryonic development. Nevertheless, in the few female FANCB mutation carriers studied so far, inactivation appeared strongly skewed towards the mutated allele [67]. This suggests that FA cells have a poor chance to survive next to unaffected cells in the same tissue, and these FA cells may therefore not give an increased cancer risk. However, the data are scarce at present so that no firm conclusions can be drawn regarding the cancer risk of female FANCB mutation carriers [60].



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