title: Development of a Targeted Multi-Disorder High-Throughput Sequencing Assay for the Effective Identification of Disease-Causing Variants.
abstract: BACKGROUND
  While next generation sequencing (NGS) is a useful tool for the identification of genetic variants to aid diagnosis and support therapy decision, high sequencing costs have limited its application within routine clinical care, especially in economically depressed areas. To investigate the utility of a multi-disease NGS based genetic test, we designed a custom sequencing assay targeting over thirty disease-associated areas including cardiac disorders, intellectual disabilities, hearing loss, collagenopathies, muscular dystrophy, Ashkenazi Jewish genetic disorders, and complex Mendelian disorders. We focused on these specific areas based on the interest of our collaborative clinical team, suggesting these diseases being the ones in need for the development of a sequencing-screening assay.
  
  
  RESULTS
  We targeted all coding, untranslated regions (UTR) and flanking intronic regions of 650 known disease-associated genes using the Roche-NimbleGen EZ SeqCapV3 capture system and sequenced on the Illumina HiSeq 2500 Rapid Run platform. Eight controls with known variants and one HapMap sample were first sequenced to assess the performance of the panel. Subsequently, as a proof of principle and to explore the possible utility of our test, we analyzed test disease subjects (n = 16). Eight had known Mendelian disorders and eight had complex pediatric diseases. In addition to assess whether copy number variation may be of utility as a companion assay relative to these specific disease areas, we used the Affymetrix Genome-Wide SNP Array 6.0 to analyze the same samples.
  
  
  CONCLUSIONS
  We identified potentially disease-associated variants: 22 missense, 4 nonsense, 1 frameshift, and 1 splice variants (16 previously identified, 12 novel among dbSNP and 15 novel among NHLBI Exome Variant Server). We found multi-disease targeted high-throughput sequencing to be a cost efficient approach in detecting disease-associated variants to aid diagnosis.
authors.affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors.forename: Maria
authors.initials: M
authors.lastname: Delio
authors.affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors.forename: Kunjan
authors.initials: K
authors.lastname: Patel
authors.affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors.forename: Alex
authors.initials: A
authors.lastname: Maslov
authors.affiliation: Divisions of Developmental Medicine & Genetics, Children's Hospital at Montefiore, Bronx, New York, United States of America.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Marion
authors.affiliation: Department of Medicine/Cardiology, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors.forename: Thomas V
authors.initials: TV
authors.lastname: McDonald
authors.affiliation: Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors.forename: Evan M
authors.initials: EM
authors.lastname: Cadoff
authors.affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors.forename: Aaron
authors.initials: A
authors.lastname: Golden
authors.affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors.forename: John M
authors.initials: JM
authors.lastname: Greally
authors.affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors.forename: Jan
authors.initials: J
authors.lastname: Vijg
authors.affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors.forename: Bernice
authors.initials: B
authors.lastname: Morrow
authors.affiliation: Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America; Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors.forename: Cristina
authors.initials: C
authors.lastname: Montagna
mesh_terms: D000328:Adult; D005260:Female; D030342:Genetic Diseases, Inborn / Q000235:genetics*; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D009154:Mutation; D020641:Polymorphism, Single Nucleotide