ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing.
Lynch syndrome (hereditary nonpolyposis colon cancer) and adenomatous polyposis syndromes frequently have overlapping clinical features. Current approaches for molecular genetic testing are often stepwise, taking a best-candidate gene approach with testing of additional genes if initial results are negative. We report a comprehensive assay called ColoSeq that detects all classes of mutations in Lynch and polyposis syndrome genes using targeted capture and massively parallel next-generation sequencing on the Illumina HiSeq2000 instrument. In blinded specimens and colon cancer cell lines with defined mutations, ColoSeq correctly identified 28/28 (100%) pathogenic mutations in MLH1, MSH2, MSH6, PMS2, EPCAM, APC, and MUTYH, including single nucleotide variants (SNVs), small insertions and deletions, and large copy number variants. There was 100% reproducibility of detection mutation between independent runs. The assay correctly identified 222 of 224 heterozygous SNVs (99.4%) in HapMap samples, demonstrating high sensitivity of calling all variants across each captured gene. Average coverage was greater than 320 reads per base pair when the maximum of 96 index samples with barcodes were pooled. In a specificity study of 19 control patients without cancer from different ethnic backgrounds, we did not find any pathogenic mutations but detected two variants of uncertain significance. ColoSeq offers a powerful, cost-effective means of genetic testing for Lynch and polyposis syndromes that eliminates the need for stepwise testing and multiple follow-up clinical visits.
Department of Laboratory Medicine, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA. cpritch@uw.edu
Colin C
CC
Pritchard
Christina
C
Smith
Stephen J
SJ
Salipante
Ming K
MK
Lee
Anne M
AM
Thornton
Alex S
AS
Nord
Cassandra
C
Gulden
Sonia S
SS
Kupfer
Elizabeth M
EM
Swisher
Robin L
RL
Bennett
Akiva P
AP
Novetsky
Gail P
GP
Jarvik
Olufunmilayo I
OI
Olopade
Paul J
PJ
Goodfellow
Mary-Claire
MC
King
Jonathan F
JF
Tait
Tom
T
Walsh
D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics; D011125:Adenomatous Polyposis Coli / Q000235:genetics*; D003123:Colorectal Neoplasms, Hereditary Nonpolyposis / Q000235:genetics*; D045647:DNA Glycosylases / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods*; D004268:DNA-Binding Proteins / Q000235:genetics; D006801:Humans; D000070957:MutL Protein Homolog 1; D051718:MutS Homolog 2 Protein / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics
D048868:Adaptor Proteins, Signal Transducing; D004268:DNA-Binding Proteins; C094443:G-T mismatch-binding protein; C501486:MLH1 protein, human; D009687:Nuclear Proteins; D045647:DNA Glycosylases; C061738:mutY adenine glycosylase; C497172:MSH2 protein, human; D000070957:MutL Protein Homolog 1; D051718:MutS Homolog 2 Protein