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Phenotype risk scores identify patients with unrecognized Mendelian disease patterns.
Bastarache L, Hughey JJ, Hebbring S, Marlo J, Zhao W, Ho WT, Van Driest SL, McGregor TL, Mosley JD, Wells QS, Temple M, Ramirez AH, Carroll R, Osterman T, Edwards T, Ruderfer D, Velez Edwards DR, Hamid R, Cogan J, Glazer A, Wei WQ, Feng Q, Brilliant M, Zhao ZJ, Cox NJ, Roden DM, Denny JC
(2018) Science 359: 1233-1239
MeSH Terms: DNA Mutational Analysis, Databases, Genetic, Electronic Health Records, Exome, Genetic Association Studies, Genetic Diseases, Inborn, Genetic Predisposition to Disease, Genetic Variation, Humans, Phenotype, Risk Factors
Show Abstract · Added March 24, 2020
Genetic association studies often examine features independently, potentially missing subpopulations with multiple phenotypes that share a single cause. We describe an approach that aggregates phenotypes on the basis of patterns described by Mendelian diseases. We mapped the clinical features of 1204 Mendelian diseases into phenotypes captured from the electronic health record (EHR) and summarized this evidence as phenotype risk scores (PheRSs). In an initial validation, PheRS distinguished cases and controls of five Mendelian diseases. Applying PheRS to 21,701 genotyped individuals uncovered 18 associations between rare variants and phenotypes consistent with Mendelian diseases. In 16 patients, the rare genetic variants were associated with severe outcomes such as organ transplants. PheRS can augment rare-variant interpretation and may identify subsets of patients with distinct genetic causes for common diseases.
Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
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Exploiting ion channel structure to assess rare variant pathogenicity.
Kroncke BM, Yang T, Kannankeril P, Shoemaker MB, Roden DM
(2018) Heart Rhythm 15: 890-894
MeSH Terms: Adolescent, Adult, Body Surface Potential Mapping, DNA, DNA Mutational Analysis, ERG1 Potassium Channel, Female, Humans, KCNQ1 Potassium Channel, Long QT Syndrome, Mutation, Pedigree, Phenotype
Show Abstract · Added March 26, 2019
BACKGROUND - A 27-year-old woman was seen for long QT syndrome. She was found to be a carrier of 2 variants, KCNQ1 Val162Met and KCNH2 Ser55Leu, and both were classified as "pathogenic" by a diagnostic laboratory, in part because of sequence proximity to other known pathogenic variants.
OBJECTIVE - The purpose of this study was to assess the relationship between both the KCNQ1 and KCNH2 variants and clinical significance using protein structure, in vitro functional assays, and familial segregation.
METHODS - We used co-segregation analysis of family, patch clamp in vitro electrophysiology, and structural analysis using recently released cryo-electron microscopy structures of both channels.
RESULTS - The structural analysis indicates that KCNQ1 Val162Met is oriented away from functionally important regions while Ser55Leu is positioned at domains critical for KCNH2 fast inactivation. Clinical phenotyping and electrophysiology study further support the conclusion that KCNH2 Ser55Leu is correctly classified as pathogenic but KCNQ1 Val162Met is benign.
CONCLUSION - Proximity in sequence space does not always translate accurately to proximity in 3-dimensional space. Emerging structural methods will add value to pathogenicity prediction.
Copyright © 2018 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.
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Molecular Defects of the Disease-Causing Human Arrestin-1 C147F Mutant.
Vishnivetskiy SA, Sullivan LS, Bowne SJ, Daiger SP, Gurevich EV, Gurevich VV
(2018) Invest Ophthalmol Vis Sci 59: 13-20
MeSH Terms: Arrestin, Cells, Cultured, DNA, DNA Mutational Analysis, Humans, Mutant Proteins, Mutation, Phosphorylation, Retinitis Pigmentosa
Show Abstract · Added March 14, 2018
Purpose - The purpose of this study was to identify the molecular defect in the disease-causing human arrestin-1 C147F mutant.
Methods - The binding of wild-type (WT) human arrestin-1 and several mutants with substitutions in position 147 (including C147F, which causes dominant retinitis pigmentosa in humans) to phosphorylated and unphosphorylated light-activated rhodopsin was determined. Thermal stability of WT and mutant human arrestin-1, as well as unfolded protein response in 661W cells, were also evaluated.
Results - WT human arrestin-1 was selective for phosphorylated light-activated rhodopsin. Substitutions of Cys-147 with smaller side chain residues, Ala or Val, did not substantially affect binding selectivity, whereas residues with bulky side chains in the position 147 (Ile, Leu, and disease-causing Phe) greatly increased the binding to unphosphorylated rhodopsin. Functional survival of mutant proteins with bulky substitutions at physiological and elevated temperature was also compromised. C147F mutant induced unfolded protein response in cultured cells.
Conclusions - Bulky Phe substitution of Cys-147 in human arrestin-1 likely causes rod degeneration due to reduced stability of the protein, which induces unfolded protein response in expressing cells.
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9 MeSH Terms
The Impact of Smoking and TP53 Mutations in Lung Adenocarcinoma Patients with Targetable Mutations-The Lung Cancer Mutation Consortium (LCMC2).
Aisner DL, Sholl LM, Berry LD, Rossi MR, Chen H, Fujimoto J, Moreira AL, Ramalingam SS, Villaruz LC, Otterson GA, Haura E, Politi K, Glisson B, Cetnar J, Garon EB, Schiller J, Waqar SN, Sequist LV, Brahmer J, Shyr Y, Kugler K, Wistuba II, Johnson BE, Minna JD, Kris MG, Bunn PA, Kwiatkowski DJ, LCMC2 investigators
(2018) Clin Cancer Res 24: 1038-1047
MeSH Terms: Adenocarcinoma of Lung, Adult, Aged, Aged, 80 and over, Antineoplastic Agents, Biomarkers, Tumor, Carcinogenesis, DNA Mutational Analysis, Female, High-Throughput Nucleotide Sequencing, Humans, Lung Neoplasms, Male, Middle Aged, Molecular Targeted Therapy, Mutation, Prognosis, Prospective Studies, Smoking, Survival Analysis, Treatment Outcome, Tumor Suppressor Protein p53, Young Adult
Show Abstract · Added April 3, 2018
Multiplex genomic profiling is standard of care for patients with advanced lung adenocarcinomas. The Lung Cancer Mutation Consortium (LCMC) is a multi-institutional effort to identify and treat oncogenic driver events in patients with lung adenocarcinomas. Sixteen U.S. institutions enrolled 1,367 patients with lung cancer in LCMC2; 904 were deemed eligible and had at least one of 14 cancer-related genes profiled using validated methods including genotyping, massively parallel sequencing, and IHC. The use of targeted therapies in patients with or p.V600E mutations, , or rearrangements, or amplification was associated with a survival increment of 1.5 years compared with those with such mutations not receiving targeted therapy, and 1.0 year compared with those lacking a targetable driver. Importantly, 60 patients with a history of smoking derived similar survival benefit from targeted therapy for alterations in //, when compared with 75 never smokers with the same alterations. In addition, coexisting mutations were associated with shorter survival among patients with , or alterations. Patients with adenocarcinoma of the lung and an oncogenic driver mutation treated with effective targeted therapy have a longer survival, regardless of prior smoking history. Molecular testing should be performed on all individuals with lung adenocarcinomas irrespective of clinical characteristics. Routine use of massively parallel sequencing enables detection of both targetable driver alterations and tumor suppressor gene and other alterations that have potential significance for therapy selection and as predictive markers for the efficacy of treatment. .
©2017 American Association for Cancer Research.
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23 MeSH Terms
Frequent BRAF mutations suggest a novel oncogenic driver in colonic neuroendocrine carcinoma.
Idrees K, Padmanabhan C, Liu E, Guo Y, Gonzalez RS, Berlin J, Dahlman KB, Beauchamp RD, Shi C
(2018) J Surg Oncol 117: 284-289
MeSH Terms: Adult, Aged, Biomarkers, Tumor, Carcinogenesis, Case-Control Studies, Colonic Neoplasms, DNA Mutational Analysis, DNA, Neoplasm, Female, Follow-Up Studies, Humans, Male, Middle Aged, Mutation, Neuroendocrine Tumors, Prognosis, Proto-Oncogene Proteins B-raf
Show Abstract · Added March 14, 2018
BACKGROUND AND OBJECTIVES - The World Health Organization (WHO) 2010 has classified GI neuroendocrine neoplasms into neuroendocrine tumor (NET) and high-grade neuroendocrine carcinoma (NEC). The genetic underpinnings of NEC are poorly understood. The aim of the study was to perform genomic profiling of NEC to better characterize this aggressive disease.
METHODS - We identified nine patients with colonic NEC between January 1, 2005 and June 30, 2013. Whole exome sequencing (WES) was performed on tumor DNA from two patients with ≥80% tumor cellularity and matched normal tissue available. Focused BRAF mutational analysis was performed on an additional seven patients via sanger sequencing of BRAF exons 11 and 15.
RESULTS - We identified BRAF exon 15 mutations (c.A1781G: p.D594G and c.T1799A: p.V600E) by WES in two patients. Upon additional screening of seven colonic NECs for BRAF exon 11 and 15 mutations, we identified BRAF V600E mutations in two of seven specimens (29%). Overall, BRAF exon 15 mutations were present in four of nine colonic NECs.
CONCLUSION - Colonic NEC is a rare but aggressive tumor with high frequency (44%) of BRAF mutations. Further investigation is warranted to ascertain the incidence of BRAF mutations in a larger population as BRAF inhibition may be a potential avenue of targeted treatment for these patients.
© 2017 Wiley Periodicals, Inc.
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17 MeSH Terms
Diagnostic value of histone 3 mutations in osteoclast-rich bone tumors.
Nohr E, Lee LH, Cates JM, Perizzolo M, Itani D
(2017) Hum Pathol 68: 119-127
MeSH Terms: Adolescent, Adult, Aged, Alberta, Biomarkers, Tumor, Bone Cysts, Aneurysmal, Bone Neoplasms, Child, Chondroblastoma, DNA Mutational Analysis, Diagnosis, Differential, Disease-Free Survival, Female, Genetic Predisposition to Disease, Giant Cell Tumor of Bone, Histones, Humans, Kaplan-Meier Estimate, Male, Middle Aged, Mutation, Osteoclasts, Phenotype, Predictive Value of Tests, Tennessee, Time Factors, Young Adult
Show Abstract · Added November 1, 2018
Differentiating osteoclast-rich lesions of bone (giant cell tumor of bone [GCTB], chondroblastoma [CBA], and aneurysmal bone cyst [ABC]) can be challenging, especially in small biopsies or fine-needle aspirations. Mutations affecting codons 34 and 36 of either H3 Histone Family Member 3A (H3F3A) and/or 3B (H3F3B) are characteristically seen in GCTB and CBAs. We devised a simple assay to identify these mutations and evaluated its applicability for routine clinical diagnosis. One hundred twenty-four tissue specimens from 108 patients (43 GCTBs, 38 CBAs and 27 ABCs) were collected from the archives of the Calgary Laboratory Services/University of Calgary and Vanderbilt University Medical Center. Histology was reviewed by an expert orthopedic pathologist. A single base extension assay (SNaPshot) is used to interrogate each nucleotide in codons 34 and 36 of H3F3A and codon 36 of H3F3B. Final diagnoses were generated after re-reviewing cases and incorporating molecular findings. Of 43 GCTBs, 38 (88%) had an H3F3A G34W mutation; 35 of 38 CBAs (92%) had a K36M mutation in either H3F3B (N = 31; 82%) or H3F3A (N = 4; 11%); none of 27 ABCs had a tested mutation. Molecular findings changed the histomorphologic diagnosis in 5 cases (3 GCTB changed to ABC, and 2 ABC changed to GCTB). These findings support the diagnostic utility of mutational analysis for this differential diagnosis in certain challenging cases when clinicoradiologic and histomorphologic features are not definitive, particularly for distinguishing cellular ABC versus GCTB with secondary ABC.
Copyright © 2017 Elsevier Inc. All rights reserved.
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A Novel Dominant Mutation in SAG, the Arrestin-1 Gene, Is a Common Cause of Retinitis Pigmentosa in Hispanic Families in the Southwestern United States.
Sullivan LS, Bowne SJ, Koboldt DC, Cadena EL, Heckenlively JR, Branham KE, Wheaton DH, Jones KD, Ruiz RS, Pennesi ME, Yang P, Davis-Boozer D, Northrup H, Gurevich VV, Chen R, Xu M, Li Y, Birch DG, Daiger SP
(2017) Invest Ophthalmol Vis Sci 58: 2774-2784
MeSH Terms: Adult, Aged, Arrestin, DNA Mutational Analysis, Exons, Female, Genes, Dominant, High-Throughput Nucleotide Sequencing, Hispanic Americans, Humans, Male, Middle Aged, Mutation, Missense, Pedigree, Retina, Retinitis Pigmentosa, Southwestern United States
Show Abstract · Added March 14, 2018
Purpose - To identify the causes of autosomal dominant retinitis pigmentosa (adRP) in a cohort of families without mutations in known adRP genes and consequently to characterize a novel dominant-acting missense mutation in SAG.
Methods - Patients underwent ophthalmologic testing and were screened for mutations using targeted-capture and whole-exome next-generation sequencing. Confirmation and additional screening were done by Sanger sequencing. Haplotypes segregating with the mutation were determined using short tandem repeat and single nucleotide variant polymorphisms. Genealogies were established by interviews of family members.
Results - Eight families in a cohort of 300 adRP families, and four additional families, were found to have a novel heterozygous mutation in the SAG gene, c.440G>T; p.Cys147Phe. Patients exhibited symptoms of retinitis pigmentosa and none showed symptoms characteristic of Oguchi disease. All families are of Hispanic descent and most were ascertained in Texas or California. A single haplotype including the SAG mutation was identified in all families. The mutation dramatically alters a conserved amino acid, is extremely rare in global databases, and was not found in 4000+ exomes from Hispanic controls. Molecular modeling based on the crystal structure of bovine arrestin-1 predicts protein misfolding/instability.
Conclusions - This is the first dominant-acting mutation identified in SAG, a founder mutation possibly originating in Mexico several centuries ago. The phenotype is clearly adRP and is distinct from the previously reported phenotypes of recessive null mutations, that is, Oguchi disease and recessive RP. The mutation accounts for 3% of the 300 families in the adRP Cohort and 36% of Hispanic families in this cohort.
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17 MeSH Terms
Genetic Evaluation and Testing of Patients and Families with Idiopathic Pulmonary Fibrosis.
Kropski JA, Young LR, Cogan JD, Mitchell DB, Lancaster LH, Worrell JA, Markin C, Liu N, Mason WR, Fingerlin TE, Schwartz DA, Lawson WE, Blackwell TS, Phillips JA, Loyd JE
(2017) Am J Respir Crit Care Med 195: 1423-1428
MeSH Terms: DNA Mutational Analysis, Genetic Testing, Humans, Idiopathic Pulmonary Fibrosis, Mutation
Added March 29, 2017
1 Communities
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5 MeSH Terms
Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma.
McFadden DG, Politi K, Bhutkar A, Chen FK, Song X, Pirun M, Santiago PM, Kim-Kiselak C, Platt JT, Lee E, Hodges E, Rosebrock AP, Bronson RT, Socci ND, Hannon GJ, Jacks T, Varmus H
(2016) Proc Natl Acad Sci U S A 113: E6409-E6417
MeSH Terms: Adenocarcinoma, Adenocarcinoma of Lung, Animals, Carcinogens, Cell Transformation, Neoplastic, DNA Copy Number Variations, DNA Mutational Analysis, Disease Models, Animal, ErbB Receptors, Gene Dosage, Genes, myc, Genes, ras, Genome-Wide Association Study, Lung Neoplasms, Mice, Mice, Transgenic, Mutation, Point Mutation, ROC Curve, Whole Exome Sequencing
Show Abstract · Added April 26, 2017
Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity.
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20 MeSH Terms
Targeted Next Generation Sequencing Identifies Markers of Response to PD-1 Blockade.
Johnson DB, Frampton GM, Rioth MJ, Yusko E, Xu Y, Guo X, Ennis RC, Fabrizio D, Chalmers ZR, Greenbowe J, Ali SM, Balasubramanian S, Sun JX, He Y, Frederick DT, Puzanov I, Balko JM, Cates JM, Ross JS, Sanders C, Robins H, Shyr Y, Miller VA, Stephens PJ, Sullivan RJ, Sosman JA, Lovly CM
(2016) Cancer Immunol Res 4: 959-967
MeSH Terms: Adult, Aged, Aged, 80 and over, Antineoplastic Agents, Immunological, B7-H1 Antigen, Biomarkers, Tumor, DNA Mutational Analysis, Female, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, High-Throughput Nucleotide Sequencing, Humans, Middle Aged, Mutation, Neoplasm Metastasis, Neoplasm Staging, Neoplasms, Prognosis, Programmed Cell Death 1 Receptor, T-Lymphocytes, Transcriptome
Show Abstract · Added April 6, 2017
Therapeutic antibodies blocking programmed death-1 and its ligand (PD-1/PD-L1) induce durable responses in a substantial fraction of melanoma patients. We sought to determine whether the number and/or type of mutations identified using a next-generation sequencing (NGS) panel available in the clinic was correlated with response to anti-PD-1 in melanoma. Using archival melanoma samples from anti-PD-1/PD-L1-treated patients, we performed hybrid capture-based NGS on 236-315 genes and T-cell receptor (TCR) sequencing on initial and validation cohorts from two centers. Patients who responded to anti-PD-1/PD-L1 had higher mutational loads in an initial cohort (median, 45.6 vs. 3.9 mutations/MB; P = 0.003) and a validation cohort (37.1 vs. 12.8 mutations/MB; P = 0.002) compared with nonresponders. Response rate, progression-free survival, and overall survival were superior in the high, compared with intermediate and low, mutation load groups. Melanomas with NF1 mutations harbored high mutational loads (median, 62.7 mutations/MB) and high response rates (74%), whereas BRAF/NRAS/NF1 wild-type melanomas had a lower mutational load. In these archival samples, TCR clonality did not predict response. Mutation numbers in the 315 genes in the NGS platform strongly correlated with those detected by whole-exome sequencing in The Cancer Genome Atlas samples, but was not associated with survival. In conclusion, mutational load, as determined by an NGS platform available in the clinic, effectively stratified patients by likelihood of response. This approach may provide a clinically feasible predictor of response to anti-PD-1/PD-L1. Cancer Immunol Res; 4(11); 959-67. ©2016 AACR.
©2016 American Association for Cancer Research.
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21 MeSH Terms