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https://www.readbyqxmd.com/read/29192238/evaluation-of-reported-pathogenic-variants-and-their-frequencies-in-a-japanese-population-based-on-a-whole-genome-reference-panel-of-2049-individuals
#1
Yumi Yamaguchi-Kabata, Jun Yasuda, Osamu Tanabe, Yoichi Suzuki, Hiroshi Kawame, Nobuo Fuse, Masao Nagasaki, Yosuke Kawai, Kaname Kojima, Fumiki Katsuoka, Sakae Saito, Inaho Danjoh, Ikuko N Motoike, Riu Yamashita, Seizo Koshiba, Daisuke Saigusa, Gen Tamiya, Shigeo Kure, Nobuo Yaegashi, Yoshio Kawaguchi, Fuji Nagami, Shinichi Kuriyama, Junichi Sugawara, Naoko Minegishi, Atsushi Hozawa, Soichi Ogishima, Hideyasu Kiyomoto, Takako Takai-Igarashi, Kengo Kinoshita, Masayuki Yamamoto
Clarifying allele frequencies of disease-related genetic variants in a population is important in genomic medicine; however, such data is not yet available for the Japanese population. To estimate frequencies of actionable pathogenic variants in the Japanese population, we examined the reported pathological variants in genes recommended by the American College of Medical Genetics and Genomics (ACMG) in our reference panel of genomic variations, 2KJPN, which was created by whole-genome sequencing of 2049 individuals of the resident cohort of the Tohoku Medical Megabank Project...
December 1, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/29179779/evaluation-of-in-silico-algorithms-for-use-with-acmg-amp-clinical-variant-interpretation-guidelines
#2
Rajarshi Ghosh, Ninad Oak, Sharon E Plon
BACKGROUND: The American College of Medical Genetics and American College of Pathologists (ACMG/AMP) variant classification guidelines for clinical reporting are widely used in diagnostic laboratories for variant interpretation. The ACMG/AMP guidelines recommend complete concordance of predictions among all in silico algorithms used without specifying the number or types of algorithms. The subjective nature of this recommendation contributes to discordance of variant classification among clinical laboratories and prevents definitive classification of variants...
November 28, 2017: Genome Biology
https://www.readbyqxmd.com/read/29179439/next-generation-sequencing-identified-novel-heterozygous-nonsense-mutation-in-cngb1-gene-associated-with-retinitis-pigmentosa-in-a-chinese-patient
#3
Santasree Banerjee, Junping Yao, Xinxin Zhang, Jianjun Niu, Zhongshan Chen
Retinitis pigmentosa (RP) is a severe hereditary eye disease characterized by progressive degeneration of photoreceptors and subsequent loss of vision. Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous group of retinal diseases. Germline mutations of CNGB1 is associated with retinitis pigmentosa. We have identified and investigated a 34-year-old Chinese man with markedly have night vision blindness and loss of midperipheral visual field. The proband also lose his far peripheral visual field and also central vision...
October 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/29131714/understanding-variations-in-secondary-findings-reporting-practices-across-u-s-genome-sequencing-laboratories
#4
Sara Ackerman, Barbara Koenig
BACKGROUND: Increasingly used for clinical purposes, genome and exome sequencing can generate clinically relevant information that is not directly related to the reason for testing (incidental or secondary findings). Debates about the ethical implications of secondary findings were sparked by the American College of Medical Genetics (ACMG)'s 2013 policy statement, which recommended that laboratories report pathogenic alterations in 56 genes. Although wide variation in laboratories' secondary findings policies has been reported, little is known about its causes...
November 13, 2017: AJOB Empirical Bioethics
https://www.readbyqxmd.com/read/29128982/actionable-secondary-findings-from-whole-genome-sequencing-of-954-east-asians
#5
Clara Sze-Man Tang, Saloni Dattani, Man-Ting So, Stacey S Cherny, Paul K H Tam, Pak C Sham, Maria-Mercè Garcia-Barcelo
Recently, the American College of Medical Genetics (ACMG) recommended the return of actionable secondary findings detected from clinical sequencing. The reported frequency of secondary findings in Asian populations were highly variable and it is unclear whether the uniformity in coverage offered by whole-genome sequencing (WGS) may impact the estimate. In this analysis, we aimed to refine the rate of secondary findings on East Asians through a large-scale WGS study. We classified 1256 protein-altering or splicing variants of the 59 actionable genes detected from WGS of 954 East Asians in strict accordance with the ACMG and the Association for Molecular Pathology guidelines...
November 11, 2017: Human Genetics
https://www.readbyqxmd.com/read/29064023/diagnostic-and-prognostic-utility-of-fluorescence-in-situ-hybridization-fish-analysis-in-acute-myeloid-leukemia
#6
REVIEW
Patrick R Gonzales, Fady M Mikhail
PURPOSE OF REVIEW: Acute myeloid leukemia (AML) is a hematologic neoplasia consisting of incompletely differentiated hematopoietic cells of the myeloid lineage that proliferate in the bone marrow, blood, and/or other tissues. Clinical implementation of fluorescence in situ hybridization (FISH) in cytogenetic laboratories allows for high-resolution analysis of recurrent structural chromosomal rearrangements specific to AML, especially in AML with normal karyotypes, which comprises approximately 33-50% of AML-positive specimens...
October 24, 2017: Current Hematologic Malignancy Reports
https://www.readbyqxmd.com/read/29048418/recommending-inclusion-of-hfe-c282y-homozygotes-in-the-acmg-actionable-gene-list-cop-out-or-stealth-move-toward-population-screening
#7
Anne-Marie Laberge
No abstract text is available yet for this article.
October 19, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29029073/clinical-genetics-and-outcome-of-left-ventricular-non-compaction-cardiomyopathy
#8
Farbod Sedaghat-Hamedani, Jan Haas, Feng Zhu, Christian Geier, Elham Kayvanpour, Martin Liss, Alan Lai, Karen Frese, Regina Pribe-Wolferts, Ali Amr, Daniel Tian Li, Omid Shirvani Samani, Avisha Carstensen, Diana Martins Bordalo, Marion Müller, Christine Fischer, Jing Shao, Jing Wang, Ming Nie, Li Yuan, Sabine Haßfeld, Christine Schwartz, Min Zhou, Zihua Zhou, Yanwen Shu, Min Wang, Kai Huang, Qiutang Zeng, Longxian Cheng, Tobias Fehlmann, Philipp Ehlermann, Andreas Keller, Christoph Dieterich, Katrin Streckfuß-Bömeke, Yuhua Liao, Michael Gotthardt, Hugo A Katus, Benjamin Meder
Aims: In this study, we aimed to clinically and genetically characterize LVNC patients and investigate the prevalence of variants in known and novel LVNC disease genes. Introduction: Left ventricular non-compaction cardiomyopathy (LVNC) is an increasingly recognized cause of heart failure, arrhythmia, thromboembolism, and sudden cardiac death. We sought here to dissect its genetic causes, phenotypic presentation and outcome. Methods and results: In our registry with follow-up of in the median 61 months, we analysed 95 LVNC patients (68 unrelated index patients and 27 affected relatives; definite familial LVNC = 23...
October 6, 2017: European Heart Journal
https://www.readbyqxmd.com/read/28950901/compound-heterozygous-mutations-in-electron-transfer-flavoprotein-dehydrogenase-identified-in-a-young-chinese-woman-with-late-onset-glutaric-aciduria-type-ii
#9
Ying Xue, Yun Zhou, Keqin Zhang, Ling Li, Abudurexiti Kayoumu, Liye Chen, Yuhui Wang, Zhiqiang Lu
BACKGROUND: Glutaric aciduria type II (GA II) is an autosomal recessive disorder affecting fatty acid and amino acid metabolism. The late-onset form of GA II disorder is almost exclusively associated with mutations in the electron transfer flavoprotein dehydrogenase (ETFDH) gene. Till now, the clinical features of late-onset GA II vary widely and pose a great challenge for diagnosis. The aim of the current study is to characterize the clinical phenotypes and genetic basis of a late-onset GAII patient...
September 26, 2017: Lipids in Health and Disease
https://www.readbyqxmd.com/read/28946813/nationwide-french-study-of-ret-variants-detected-from-2003-to-2013-suggests-a-possible-influence-of-polymorphisms-as-modifiers
#10
Maylis Lebeault, Stéphane Pinson, Marine Guillaud-Bataille, Anne-Paule Gimenez-Roqueplo, Alain Carrie, Véronique Barbu, Pascal Pigny, Stéphane Bezieau, Jean-Marc Rey, Chantal Delvincourt, Sophie Giraud, Charlotte Veyrat-Durebex, Patrick Saulnier, Nathalie Bouzamondo, Marie Chabbert, Julien Blin, Amira Mohamed, Pauline Romanet, Francoise Borson-Chazot, Vincent Rohmer, Anne Barlier, Delphine Mirebeau-Prunier
BACKGROUND: The presence of single nucleotide polymorphisms (SNPs) in the REarranged during Transfection (RET) gene has been investigated with regard to their potential role in the development or progression of medullary thyroid cancer or pheochromocytomas (PHEO) in patients with the multiple endocrine neoplasia type 2 (MEN2) syndrome. The aim of this study was to evaluate the spectrum of RET variants in France between 2003 and 2013, and to evaluate the impact of SNPs on the MEN2 A phenotype...
November 3, 2017: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/28944235/assessing-risk-for-mendelian-disorders-in-a-bronx-population
#11
Guy diSibio, Kinnari Upadhyay, Philip Meyer, Carole Oddoux, Harry Ostrer
BACKGROUND: To identify variants likely responsible for Mendelian disorders among the three major ethnic groups in the Bronx that might be useful to include in genetic screening panels or whole exome sequencing filters and to estimate their likely prevalence in these populations. METHODS: Variants from a high-density oligonucleotide screen of 192 members from each of the three ethnic-national populations (African Americans, Puerto Ricans, and Dominicans) were evaluated for overlap with next generation sequencing data...
September 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28903413/a-novel-heterozygous-germline-deletion-in-msh2-gene-in-a-five-generation-chinese-family-with-lynch-syndrome
#12
Bin Wu, Wuyang Ji, Shengran Liang, Chao Ling, Yan You, Lai Xu, Min-Er Zhong, Yi Xiao, Hui-Zhong Qiu, Jun-Yang Lu, Santasree Banerjee
Lynch syndrome (LS) is one of the most common familial forms of colorectal cancer predisposing syndrome with an autosomal dominant mode of inheritance. LS is caused by the germline mutations in DNA mismatch repair (MMR) genes including MSH2, MLH1, MSH6 and PMS2. Clinically, LS is characterized by high incidence of early-onset colorectal cancer as well as endometrial, small intestinal and urinary tract cancers, usually occur in the third to fourth decade of the life. Here we describe a five generation Chinese family with LS clinically diagnosed according to the Amsterdam II criteria...
August 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28867359/novel-heterozygous-notch3-pathogenic-variant-found-in-two-chinese-patients-with-cadasil
#13
Shufeng Li, Yifan Chen, Haitao Shan, Fang Ma, Minke Shi, Jun Xue
NOTCH3 mutations have been described to cause cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). Here, we report 2 CADASIL patients from a Chinese family. Whole genome sequencing was performed on the two CADASIL patients. The novel variant c.128G>C in exon 2 of NOTCH3 was identified and confirmed through PCR-Sanger sequencing (Human Genome Variation Society nomenclature: HGVS: NOTCH3 c.128G>C; p.Cys43Ser). The heterozygous NOTCH3 variant cause a cysteine to serine substitution at codon 43...
December 2017: Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia
https://www.readbyqxmd.com/read/28782058/consistency-of-brca1-and-brca2-variant-classifications-among-clinical-diagnostic-laboratories
#14
Stephen E Lincoln, Shan Yang, Melissa S Cline, Yuya Kobayashi, Can Zhang, Scott Topper, David Haussler, Benedict Paten, Robert L Nussbaum
BACKGROUND: Genetic tests of the cancer predisposition genes BRCA1 and BRCA2 inform significant clinical decisions for both physicians and patients. Most uncovered variants are benign, and determining which few are pathogenic (disease-causing) is sometimes challenging and can potentially be inconsistent among laboratories. The ClinVar database makes de-identified clinical variant classifications from multiple laboratories publicly available for comparison and review, per recommendations of the American Medical Association (AMA), the American College of Medical Genetics (ACMG), the National Society for Genetic Counselors (NSGC), and other organizations...
July 2017: JCO Precision Oncology
https://www.readbyqxmd.com/read/28732364/a-novel-heterozygous-germline-deletion-in-msh2-gene-in-a-five-generation-chinese-family-with-lynch-syndrome
#15
Bin Wu, Wuyang Ji, Shengran Liang, Chao Ling, Yan You, Lai Xu, Min-Er Zhong, Yi Xiao, Hui-Zhong Qiu, Jun-Yang Lu, Santasree Banerjee
Lynch syndrome (LS) is one of the most common familial forms of colorectal cancer predisposing syndrome with an autosomal dominant mode of inheritance. LS is caused by the germline mutations in DNA mismatch repair (MMR) genes including MSH2, MLH1, MSH6and PMS2. Clinically, LS is characterized by high incidence of early-onset colorectal cancer as well as endometrial, small intestinal and urinary tract cancers, usually occur in the third to fourth decade of the life. Here we describe a five generation Chinese family with LS clinically diagnosed according to the Amsterdam II criteria...
July 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28726804/diagnostic-cytogenetic-testing-following-positive-noninvasive-prenatal-screening-results-a-clinical-laboratory-practice-resource-of-the-american-college-of-medical-genetics-and-genomics-acmg
#16
Athena M Cherry, Yassmine M Akkari, Kimberly M Barr, Hutton M Kearney, Nancy C Rose, Sarah T South, James H Tepperberg, Jeanne M Meck
Disclaimer: ACMG Clinical Laboratory Practice Resources are developed primarily as an educational tool for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these practice resources is voluntary and does not necessarily assure a successful medical outcome. This Clinical Laboratory Practice Resource should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results...
August 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28706611/a-novel-variant-in-the-pah-gene-causing-phenylketonuria-in-an-iranian-pedigree
#17
Elaheh Alavinejad, Seyede Zahra Sajedi, Masoumeh Razipour, Mona Entezam, Neda Mohajer, Aria Setoodeh, Saeed Talebi, Mohammad Keramatipour
BACKGROUND: Phenylalanine hydroxylase (PAH) gene is the well-known causative gene for classic Phenylketonuria (PKU) (OMIM#261600) disease, with more than 500 reported mutations. Through this study, a novel mutation in the PAH gene in an Iranian pedigree with phenylketonuria was introduced. METHODS: A consanguineous family with a 10-year old affected girl was referred for genetic analysis. Mutation screening of all exons and exon-intron boundaries was performed by Sanger sequencing, and mini haplotype analysis was carried out by genotyping of Short Tandem Repeat (STR) and Variable Number Tandem Repeat (VNTR) alleles...
July 2017: Avicenna Journal of Medical Biotechnology
https://www.readbyqxmd.com/read/28689263/variation-among-consent-forms-for-clinical-whole-exome-sequencing
#18
Sara A Fowler, Carol J Saunders, Mark A Hoffman
The goal of this study was to explore variation among informed consent documents for clinical whole exome sequencing (WES) in order to identify the level of consistency with the recommendations from the American College of Medical Genetics and Genomics (ACMG) and the Presidential Commission for the Study of Bioethical Issues (Bioethics Commission) regarding informed consent for clinical WES. Recommendations were organized into a framework of key points for analysis. Content analysis was conducted on a sample of informed consent documents for clinical WES downloaded from 18 laboratory websites...
July 8, 2017: Journal of Genetic Counseling
https://www.readbyqxmd.com/read/28682309/laboratory-diagnosis-of-biotinidase-deficiency-2017-update-a-technical-standard-and-guideline-of-the-american-college-of-medical-genetics-and-genomics
#19
Erin T Strovel, Tina M Cowan, Anna I Scott, Barry Wolf
Disclaimer: These ACMG Standards and Guidelines are intended as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these Standards and Guidelines is voluntary and does not necessarily assure a successful medical outcome. These Standards and Guidelines should not be considered inclusive of all proper procedures and tests or exclusive of others that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, clinical laboratory geneticists should apply their professional judgment to the specific circumstances presented by the patient or specimen...
October 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28671958/clinical-genome-sequencing-and-population-preferences-for-information-about-incidental-findings-from-medically-actionable-genes-mags-to-patient-actionable-genes-pags
#20
Thomas Ploug, Søren Holm
Whole genome or exome sequencing is increasingly used in the clinical contexts, and 'incidental' findings are generated. There is need for an adequate policy for the reporting of these findings to individuals. Such a policy has been suggested by the American College of Medical Genetics and Genomics (ACMG). We argue that ACMG's policy is overly paternalistic, and that an adequate policy must take into account population preferences. We conducted a choice based conjoint survey of population preferences for reporting in a representative sample of the Danish population...
2017: PloS One
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