title: Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia.
abstract: Current methods for detecting mutations in Fanconi anemia (FA)-suspected patients are inefficient and often miss mutations. We have applied recent advances in DNA sequencing and genomic capture to the diagnosis of FA. Specifically, we used custom molecular inversion probes or TruSeq-enrichment oligos to capture and sequence FA and related genes, including introns, from 27 samples from the International Fanconi Anemia Registry at The Rockefeller University. DNA sequencing was complemented with custom array comparative genomic hybridization (aCGH) and RNA sequencing (RNA-seq) analysis. aCGH identified deletions/duplications in 4 different FA genes. RNA-seq analysis revealed lack of allele specific expression associated with a deletion and splicing defects caused by missense, synonymous, and deep-in-intron variants. The combination of TruSeq-targeted capture, aCGH, and RNA-seq enabled us to identify the complementation group and biallelic germline mutations in all 27 families: FANCA (7), FANCB (3), FANCC (3), FANCD1 (1), FANCD2 (3), FANCF (2), FANCG (2), FANCI (1), FANCJ (2), and FANCL (3). FANCC mutations are often the cause of FA in patients of Ashkenazi Jewish (AJ) ancestry, and we identified 2 novel FANCC mutations in 2 patients of AJ ancestry. We describe here a strategy for efficient molecular diagnosis of FA.
authors.affiliation: Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. chandra@mail.nih.gov.
authors.forename: Settara C
authors.initials: SC
authors.lastname: Chandrasekharappa
authors.forename: Francis P
authors.initials: FP
authors.lastname: Lach
authors.forename: Danielle C
authors.initials: DC
authors.lastname: Kimble
authors.forename: Aparna
authors.initials: A
authors.lastname: Kamat
authors.forename: Jamie K
authors.initials: JK
authors.lastname: Teer
authors.forename: Frank X
authors.initials: FX
authors.lastname: Donovan
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Flynn
authors.forename: Shurjo K
authors.initials: SK
authors.lastname: Sen
authors.forename: Supawat
authors.initials: S
authors.lastname: Thongthip
authors.forename: Erica
authors.initials: E
authors.lastname: Sanborn
authors.forename: Agata
authors.initials: A
authors.lastname: Smogorzewska
authors.forename: Arleen D
authors.initials: AD
authors.lastname: Auerbach
authors.forename: Elaine A
authors.initials: EA
authors.lastname: Ostrander
mesh_terms: D050976:Basic-Leucine Zipper Transcription Factors / Q000235:genetics; D055028:Comparative Genomic Hybridization / Q000379:methods*; D005192:Family Health; D005199:Fanconi Anemia / Q000175:diagnosis* / Q000208:ethnology / Q000235:genetics*; D052217:Fanconi Anemia Complementation Group A Protein / Q000235:genetics; D052218:Fanconi Anemia Complementation Group C Protein / Q000235:genetics; D052236:Fanconi Anemia Complementation Group D2 Protein / Q000235:genetics; D052241:Fanconi Anemia Complementation Group G Protein / Q000235:genetics; D052240:Fanconi Anemia Complementation Group L Protein / Q000235:genetics; D051856:Fanconi Anemia Complementation Group Proteins / Q000235:genetics; D017353:Gene Deletion; D020440:Gene Duplication; D006801:Humans; D007585:Jews / Q000235:genetics*; D009154:Mutation; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: C102108:BACH1 protein, human; D050976:Basic-Leucine Zipper Transcription Factors; C498471:FANCA protein, human; C515775:FANCB protein, human; C497651:FANCC protein, human; C499905:FANCD2 protein, human; C499909:FANCG protein, human; C519921:FANCI protein, human; D052217:Fanconi Anemia Complementation Group A Protein; D052218:Fanconi Anemia Complementation Group C Protein; D052236:Fanconi Anemia Complementation Group D2 Protein; D052241:Fanconi Anemia Complementation Group G Protein; D051856:Fanconi Anemia Complementation Group Proteins; C499908:FANCL protein, human; D052240:Fanconi Anemia Complementation Group L Protein