Genetic diagnosis by whole exome capture and massively parallel DNA sequencing.
Protein coding genes constitute only approximately 1% of the human genome but harbor 85% of the mutations with large effects on disease-related traits. Therefore, efficient strategies for selectively sequencing complete coding regions (i.e., "whole exome") have the potential to contribute to the understanding of rare and common human diseases. Here we report a method for whole-exome sequencing coupling Roche/NimbleGen whole exome arrays to the Illumina DNA sequencing platform. We demonstrate the ability to capture approximately 95% of the targeted coding sequences with high sensitivity and specificity for detection of homozygous and heterozygous variants. We illustrate the utility of this approach by making an unanticipated genetic diagnosis of congenital chloride diarrhea in a patient referred with a suspected diagnosis of Bartter syndrome, a renal salt-wasting disease. The molecular diagnosis was based on the finding of a homozygous missense D652N mutation at a position in SLC26A3 (the known congenital chloride diarrhea locus) that is virtually completely conserved in orthologues and paralogues from invertebrates to humans, and clinical follow-up confirmed the diagnosis. To our knowledge, whole-exome (or genome) sequencing has not previously been used to make a genetic diagnosis. Five additional patients suspected to have Bartter syndrome but who did not have mutations in known genes for this disease had homozygous deleterious mutations in SLC26A3. These results demonstrate the clinical utility of whole-exome sequencing and have implications for disease gene discovery and clinical diagnosis.
Choi
Murim
M
Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA.
Scholl
Ute I
UI
Ji
Weizhen
W
Liu
Tiewen
T
Tikhonova
Irina R
IR
Zumbo
Paul
P
Nayir
Ahmet
A
Bakkaloğlu
Ayşin
A
Ozen
Seza
S
Sanjad
Sami
S
Nelson-Williams
Carol
C
Farhi
Anita
A
Mane
Shrikant
S
Lifton
Richard P
RP
D000465:Algorithms; D017920:Antiporters / Q000235:genetics; D001483:Base Sequence; D027963:Chloride-Bicarbonate Antiporters; D002712:Chlorides; D019295:Computational Biology; D003967:Diarrhea / Q000235:genetics; D030342:Genetic Diseases, Inborn / Q000235:genetics*; D023281:Genomics / Q000379:methods; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D008969:Molecular Sequence Data; D020125:Mutation, Missense / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D000076988:Sulfate Transporters
D017920:Antiporters; D027963:Chloride-Bicarbonate Antiporters; D002712:Chlorides; C081011:SLC26A3 protein, human; D000076988:Sulfate Transporters