title: Carrier testing for severe childhood recessive diseases by next-generation sequencing.
abstract: Of 7028 disorders with suspected Mendelian inheritance, 1139 are recessive and have an established molecular basis. Although individually uncommon, Mendelian diseases collectively account for ~20% of infant mortality and ~10% of pediatric hospitalizations. Preconception screening, together with genetic counseling of carriers, has resulted in remarkable declines in the incidence of several severe recessive diseases including Tay-Sachs disease and cystic fibrosis. However, extension of preconception screening to most severe disease genes has hitherto been impractical. Here, we report a preconception carrier screen for 448 severe recessive childhood diseases. Rather than costly, complete sequencing of the human genome, 7717 regions from 437 target genes were enriched by hybrid capture or microdroplet polymerase chain reaction, sequenced by next-generation sequencing (NGS) to a depth of up to 2.7 gigabases, and assessed with stringent bioinformatic filters. At a resultant 160x average target coverage, 93% of nucleotides had at least 20x coverage, and mutation detection/genotyping had ~95% sensitivity and ~100% specificity for substitution, insertion/deletion, splicing, and gross deletion mutations and single-nucleotide polymorphisms. In 104 unrelated DNA samples, the average genomic carrier burden for severe pediatric recessive mutations was 2.8 and ranged from 0 to 7. The distribution of mutations among sequenced samples appeared random. Twenty-seven percent of mutations cited in the literature were found to be common polymorphisms or misannotated, underscoring the need for better mutation databases as part of a comprehensive carrier testing strategy. Given the magnitude of carrier burden and the lower cost of testing compared to treating these conditions, carrier screening by NGS made available to the general population may be an economical way to reduce the incidence of and ameliorate suffering associated with severe recessive childhood disorders.
authors.affiliation: National Center for Genome Resources, Santa Fe, NM 87505, USA.
authors.forename: Callum J
authors.initials: CJ
authors.lastname: Bell
authors.forename: Darrell L
authors.initials: DL
authors.lastname: Dinwiddie
authors.forename: Neil A
authors.initials: NA
authors.lastname: Miller
authors.forename: Shannon L
authors.initials: SL
authors.lastname: Hateley
authors.forename: Elena E
authors.initials: EE
authors.lastname: Ganusova
authors.forename: Joann
authors.initials: J
authors.lastname: Mudge
authors.forename: Ray J
authors.initials: RJ
authors.lastname: Langley
authors.forename: Lu
authors.initials: L
authors.lastname: Zhang
authors.forename: Clarence C
authors.initials: CC
authors.lastname: Lee
authors.forename: Faye D
authors.initials: FD
authors.lastname: Schilkey
authors.forename: Vrunda
authors.initials: V
authors.lastname: Sheth
authors.forename: Jimmy E
authors.initials: JE
authors.lastname: Woodward
authors.forename: Heather E
authors.initials: HE
authors.lastname: Peckham
authors.forename: Gary P
authors.initials: GP
authors.lastname: Schroth
authors.forename: Ryan W
authors.initials: RW
authors.lastname: Kim
authors.forename: Stephen F
authors.initials: SF
authors.lastname: Kingsmore
mesh_terms: D001483:Base Sequence; D002648:Child; D030541:Databases, Genetic; D005260:Female; D005808:Genes, Recessive / Q000235:genetics*; D006580:Genetic Carrier Screening / Q000379:methods*; D005820:Genetic Testing / Q000191:economics / Q000379:methods*; D015894:Genome, Human; D006579:Heterozygote; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation; D011247:Pregnancy; D011296:Prenatal Diagnosis; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods*