Automating sequence-based detection and genotyping of SNPs from diploid samples

Stephens, Matthew; Sloan, James S.; Robertson, Peggy D.; Scheet, Paul; Nickerson, Deborah A.

doi:10.1038/ng1746

Cited by 138 publications

(118 citation statements)

References 16 publications

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“…SNPs were called by using PolyPhred 6.02b (37,38) followed by a postprocessing pipeline we refer to as SNPCompare. In brief, we retain all SNPs called by PolyPhred with a confidence of 99.…”

Section: Methodsmentioning

confidence: 99%

Drug-sensitiveFGFR2mutations in endometrial carcinoma

Dutt

Salvesen

Chen

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

323

283

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Oncogenic activation of tyrosine kinases is a common mechanism of carcinogenesis and, given the druggable nature of these enzymes, an attractive target for anticancer therapy. Here, we show that somatic mutations of the fibroblast growth factor receptor 2 (FGFR2) tyrosine kinase gene, FGFR2, are present in 12% of endometrial carcinomas, with additional instances found in lung squamous cell carcinoma and cervical carcinoma. These FGFR2 mutations, many of which are identical to mutations associated with congenital craniofacial developmental disorders, are constitutively activated and oncogenic when ectopically expressed in NIH 3T3 cells. Inhibition of FGFR2 kinase activity in endometrial carcinoma cell lines bearing such FGFR2 mutations inhibits transformation and survival, implicating FGFR2 as a novel therapeutic target in endometrial carcinoma.endometrial cancer ͉ fibroblast growth factor receptor 2 ͉ oncogene ͉ targeted therapy ͉ tyrosine kinase T yrosine kinases play a major role in transduction of proliferative signals and can become oncogenic when deregulated by somatic mutation (1). Somatically altered tyrosine kinases have proven to be tractable therapeutic targets in several tumor types; examples of successfully targeted tyrosine kinases include ABL1 in chronic myeloid leukemia (2), KIT in gastrointestinal stromal tumors (3), ERBB2 in breast cancer (4), and EGFR in non-small-cell lung cancer (5-7). The tyrosine kinase family has not been exhaustively studied in human cancer, and it is likely that additional tyrosine kinase therapeutic targets remain to be discovered.The fibroblast growth factor receptor (FGFR) tyrosine kinase family, which is comprised of four kinases that differentially respond to 18 FGF ligands (8, 9), has long been implicated in cancer. Translocations involving FGFR3, and activating somatic mutations in FGFR3, have been identified in multiple myeloma patients (10, 11), and translocations of FGFR1 have been found in patients with 8p11 myeloproliferative syndrome (12). Isolated cases of a missense mutation of FGFR4 in a lung adenocarcinoma patient and missense mutations of FGFR2 in a lung squamous cell carcinoma patient and gastric cancer patient have also been reported (13,14). In addition to these documented examples of somatic mutation of FGFR family members in cancer, a germ-line polymorphism in the second intron of FGFR2 was found to be associated with breast cancer in genomewide association studies (15,16).FGFR1-FGFR3 are characterized by alternative splicing of the mRNA encoding the third Ig-like repeat in the extracellular ligand-binding domain. This differential splicing determines ligand specificity such that isoforms expressed primarily in epithelial cells (IIIb) preferentially bind FGF ligands expressed by mesenchymal cells, and isoforms expressed primarily in mesenchymal cells (IIIc) preferentially bind FGF ligands expressed by epithelial cells (17)(18)(19). Alteration of this restricted expression pattern can lead to oncogenic transformation (20). Mutations in FGFR2 and FGF...

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Section: Methodsmentioning

confidence: 99%

Drug-sensitiveFGFR2mutations in endometrial carcinoma

Dutt

Salvesen

Chen

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

323

283

View full text Add to dashboard Cite

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“…All sequences for a given PCR product are then assembled using consed (Gordon et al 1998); groups of sequences derived from overlapping PCR products are assembled independently, which allows for independent cross-validation of the overlapping regions. Sequence variants, including singlenucleotide differences and short (<100 base) insertions and deletions, are identified using PolyPhred v6.11 (Bhangale et al 2006;Stephens et al 2006). Variants within genes are classified as residing within the untranslated regions (59 and 39 UTRs), within introns, or within protein-coding regions (with predicted gene structures based on UCSC Genome Browser annotations).…”

Section: Sequence Analysis and Variant Detectionmentioning

confidence: 99%

The ClinSeq Project: Piloting large-scale genome sequencing for research in genomic medicine

Biesecker¹,

Mullikin²,

Facio³

et al. 2009

Genome Res.

237

240

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ClinSeq is a pilot project to investigate the use of whole-genome sequencing as a tool for clinical research. By piloting the acquisition of large amounts of DNA sequence data from individual human subjects, we are fostering the development of hypothesis-generating approaches for performing research in genomic medicine, including the exploration of issues related to the genetic architecture of disease, implementation of genomic technology, informed consent, disclosure of genetic information, and archiving, analyzing, and displaying sequence data. In the initial phase of ClinSeq, we are enrolling roughly 1000 participants; the evaluation of each includes obtaining a detailed family and medical history, as well as a clinical evaluation. The participants are being consented broadly for research on many traits and for wholegenome sequencing. Initially, Sanger-based sequencing of 300-400 genes thought to be relevant to atherosclerosis is being performed, with the resulting data analyzed for rare, high-penetrance variants associated with specific clinical traits. The participants are also being consented to allow the contact of family members for additional studies of sequence variants to explore their potential association with specific phenotypes. Here, we present the general considerations in designing ClinSeq, preliminary results based on the generation of an initial 826 Mb of sequence data, the findings for several genes that serve as positive controls for the project, and our views about the potential implications of ClinSeq. The early experiences with ClinSeq illustrate how large-scale medical sequencing can be a practical, productive, and critical component of research in genomic medicine.

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“…The PCR products were sequenced using standard dye primer and termination chemistry on an ABI 3730. Polymorphisms were identified using PolyPhred 5.0 (29). Analysts reviewed all polymorphisms identified by PolyPhred for falsepositives associated with features of the surrounding sequence or biochemical artifacts.…”

Section: Sequencing and Genotypingmentioning

confidence: 99%

A common VLDLR polymorphism interacts with APOE genotype in the prediction of carotid artery disease risk

Crawford

Nord

Badzioch

et al. 2008

Journal of Lipid Research

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The genetic factors associated with carotid artery disease (CAAD) are not fully known. Because of its role in lipid metabolism, we hypothesized that common genetic variation in the very low density lipoprotein receptor (VLDLR) gene is associated with severe CAAD (.80% stenosis), body mass index (BMI), and lipid traits in humans. VLDLR was resequenced for variation discovery in 92 subjects, and single nucleotide polymorphisms (tagSNPs) were chosen for genotyping in a larger cohort (n 5 1,027). Of the 17 tagSNPs genotyped, one tagSNP (SNP 1226; rs1454626) located in the 5 ¶ flanking region of VLDLR was associated with CAAD, BMI, and LDL-associated apolipoprotein B (apoB). We also identified receptor-ligand genetic interactions between VLDLR 1226 and APOE genotype for predicting CAAD case status. These findings may further our understanding of VLDLR function, its ligand APOE, and ultimately the pathogenesis of CAAD in the general popu-

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Automating sequence-based detection and genotyping of SNPs from diploid samples

Cited by 138 publications

References 16 publications

Drug-sensitiveFGFR2mutations in endometrial carcinoma

Drug-sensitiveFGFR2mutations in endometrial carcinoma

The ClinSeq Project: Piloting large-scale genome sequencing for research in genomic medicine

A common VLDLR polymorphism interacts with APOE genotype in the prediction of carotid artery disease risk

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