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Journal of Human Genetics

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https://www.readbyqxmd.com/read/28202952/imputation-approach-for-deducing-a-complete-mitogenome-sequence-from-low-depth-coverage-next-generation-sequencing-data-application-to-ancient-remains-from-the-moon-pyramid-mexico
#1
Fuzuki Mizuno, Masahiko Kumagai, Kunihiko Kurosaki, Michiko Hayashi, Saburo Sugiyama, Shintaroh Ueda, Li Wang
It is considered that more than 15 depths of coverage are necessary for next-generation sequencing (NGS) data to obtain reliable complete nucleotide sequences of the mitogenome. However, it is difficult to satisfy this requirement for all nucleotide positions because of problems obtaining a uniform depth of coverage for poorly preserved materials. Thus, we propose an imputation approach that allows a complete mitogenome sequence to be deduced from low-depth-coverage NGS data. We used different types of mitogenome data files as panels for imputation: a worldwide panel comprising all the major haplogroups, a worldwide panel comprising sequences belonging to the estimated haplogroup alone, a panel comprising sequences from the population most closely related to an individual under investigation, and a panel comprising sequences belonging to the estimated haplogroup from the population most closely related to an individual under investigation...
February 16, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28202951/erratum-pars2-and-nars2-mutations-in-infantile-onset-neurodegenerative-disorder
#2
Takeshi Mizuguchi, Mitsuko Nakashima, Mitsuhiro Kato, Keitaro Yamada, Tohru Okanishi, Nina Ekhilevitch, Hanna Mandel, Ayelet Eran, Miyuki Toyono, Yukio Sawaishi, Hirotaka Motoi, Masaaki Shiina, Kazuhiro Ogata, Satoko Miyatake, Noriko Miyake, Hirotomo Saitsu, Naomichi Matsumoto
No abstract text is available yet for this article.
February 16, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28202950/including-non-informative-parents-in-transmission-based-association-tests
#3
Hemant Kulkarni, Saurabh Ghosh
The classical transmission disequilibrium test (TDT) based on a trio design uses information only on the allele transmitted by a heterozygous parent at a marker locus as homozygous parents are non-informative about linkage. However, the phenotype of an offspring depends on the alleles transmitted by both parents, irrespective of whether the parents are homozygous or heterozygous, and hence carry useful information on association. In this article, we propose modifications to the TDT procedures by incorporating transmission data on both parents in an informative trio to explore possible gain in power in detecting association...
February 16, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28202949/clinical-diversity-caused-by-novel-ighmbp2-variants
#4
Jun-Hui Yuan, Akihiro Hashiguchi, Akiko Yoshimura, Hiroshi Yaguchi, Koji Tsuzaki, Azusa Ikeda, Kenji Wada-Isoe, Masahiro Ando, Tomonori Nakamura, Yujiro Higuchi, Yu Hiramatsu, Yuji Okamoto, Hiroshi Takashima
Immunoglobulin helicase μ-binding protein 2 (IGHMBP2) gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). From June 2014 to December 2015, we collected 408 cases, who referred to our genetic laboratory for genetic analysis, suspected with CMT disease or other inherited peripheral neuropathies (IPNs) on the basis of clinical manifestations and electrophysiological studies. Mutation screening was performed using Ion AmpliSeq Custom Panels, which comprise 72 disease-causing or candidate genes of IPNs...
February 16, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28202948/identification-of-pathogenic-variants-in-genes-related-to-channelopathy-and-cardiomyopathy-in-korean-sudden-cardiac-arrest-survivors
#5
Ju Sun Song, Jong-Sun Kang, Young-Eun Kim, Seung-Jung Park, Kyoung-Min Park, June Huh, June Soo Kim, Hana Cho, Chang-Seok Ki, Young Keun On
Pathogenic variants in genes related to channelopathy and cardiomyopathy are the most common cause of sudden unexplained cardiac death. However, few reports have investigated the frequency and/or spectrum of pathogenic variants in these genes in Korean sudden cardiac arrest survivors. This study aimed to investigate the causative genetic variants of cardiac-associated genes in Korean sudden cardiac arrest survivors. We performed exome sequencing followed by filtering and validation of variants in 100 genes related to channelopathy and cardiomyopathy in 19 Korean patients who survived sudden cardiac arrest...
February 16, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28179634/rapid-and-cost-effective-high-throughput-sequencing-for-identification-of-germline-mutations-of-brca1-and-brca2
#6
Somayeh Ahmadloo, Hirofumi Nakaoka, Takahide Hayano, Kazuyoshi Hosomichi, Hua You, Emi Utsuno, Takafumi Sangai, Motoi Nishimura, Kazuyuki Matsushita, Akira Hata, Fumio Nomura, Ituro Inoue
Genetic testing for breast cancer predisposing genes, BRCA1 and BRCA2, can take advantage for early identification of carriers with pathogenic germline mutations. However, conventional approaches based on Sanger sequencing are laborious and expensive. Next-generation sequencing technology has a great impact on investigation of medical genomics and now applied clinical genetics. We provide a protocol based on a pool and capture method followed by high-throughput sequencing, which realizes a rapid, high-quality, high-accuracy and low-cost testing for mutations in BRCA1 and BRCA2 by using small amounts of input DNA...
February 9, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28179633/band-like-calcification-with-simplified-gyration-and-polymicrogyria-report-of-10-new-families-and-identification-of-five-novel-ocln-mutations
#7
Mohamed S Abdel-Hamid, Ghada M H Abdel-Salam, Mahmoud Y Issa, Bayoumi A Emam, Maha S Zaki
Band-like calcification with simplified gyration and polymicrogyria (BLC-PMG) is an extremely rare autosomal recessive disorder with distinctive clinical and neuroimaging findings. To date, only 17 patients from 9 unrelated families with BLC-PMG have been reported worldwide. Herein, we describe a series of 13 new patients derived from 10 unrelated Egyptian families. Patients presented at early life with the classic phenotype including severe microcephaly, failure to acquire developmental skills, growth failure and the distinguished calcification patterns involving the cortex, thalami, basal ganglia and pons...
February 9, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28148926/single-nucleotide-variant-proportion-in-genes-a-new-concept-to-explore-major-depression-based-on-dna-sequencing-data
#8
Chenglong Yu, Bernhard T Baune, Julio Licinio, Ma-Li Wong
Major depressive disorder (MDD) is a common psychiatric illness with significant medical and socioeconomic impact. Genetic factors are likely to play important roles in the development of this condition. DNA sequencing technology has the ability to identify all private genetic mutations and provides new channels for studying the biology of MDD. In this proof-of-concept study we proposed a novel concept, single-nucleotide variant proportion (SNVP), to investigate MDD based on whole-genome sequencing (WGS) data...
February 2, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28148925/a-novel-mutation-in-the-proteolytic-domain-of-lonp1-causes-atypical-codas-syndrome
#9
Takehiko Inui, Mai Anzai, Yusuke Takezawa, Wakaba Endo, Yosuke Kakisaka, Atsuo Kikuchi, Akira Onuma, Shigeo Kure, Ichizo Nishino, Chihiro Ohba, Hirotomo Saitsu, Naomichi Matsumoto, Kazuhiro Haginoya
Cerebral, ocular, dental, auricular, skeletal (CODAS) syndrome is a rare autosomal recessive multisystem disorder caused by mutations in LONP1. It is characterized by intellectual disability, cataracts, delayed tooth eruption, malformed auricles and skeletal abnormalities. We performed whole-exome sequencing on a 12-year-old Japanese male with severe intellectual disability, congenital bilateral cataracts, spasticity, hypotonia with motor regression and progressive cerebellar atrophy with hyperintensity of the cerebellar cortex on T2-weighted images...
February 2, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28148924/mutations-in-methionyl-trna-synthetase-gene-in-a-chinese-family-with-interstitial-lung-and-liver-disease-postnatal-growth-failure-and-anemia
#10
Yu Sun, Guorui Hu, Jihang Luo, Di Fang, Yongguo Yu, Xiang Wang, Jing Chen, Wenjuan Qiu
Methionyl-tRNA synthetase (MARS) catalyzes the ligation of methionine to tRNA. Heterozygous MARS mutations have been reported to cause Charcot-Marie-Tooth disease, axonal, type 2U (CMT2U). Homozygous or compound heterozygous mutations in MARS gene would cause interstitial lung and liver disease (ILLD), a severe disease onset in infancy or early childhood. Here we report a Chinese ILLD family with two affected boys diagnosed by exome sequencing. They carry novel compound heterozygous MARS mutations (p.Asp145Asn and p...
February 2, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28148923/to-aggregate-or-not-that-is-the-question-a-commentary-on-single-nucleotide-variant-proportion-in-genes-a-new-concept-to-explore-major-depression-based-on-dna-sequencing-data
#11
https://www.readbyqxmd.com/read/28148922/detecting-disease-association-with-rare-variants-in-case-parents-studies
#12
Yu-Mei Li, Yang Xiang
Major advances in DNA sequencing technology have generated large quantities of sequence data that promote the development of statistical methods for rare variant association analyses. Although many population-based case control methods have been well developed for rare variant analysis, little work focuses on family-based studies. In this paper, we extend the existing methods to test for association of rare variants with case-parents data. We investigated the influence of non-variants and effects of causal variants on max-, multi-marker test, and collapsing method, and proposed an adaptive strategy based on a difference vector...
February 2, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28148921/subdivisions-of-haplogroups-u-and-c-encompass-mitochondrial-dna-lineages-of-eneolithic-early-bronze-age-kurgan-populations-of-western-north-pontic-steppe
#13
Alexey G Nikitin, Svetlana Ivanova, Dmytro Kiosak, Jessica Badgerow, Jeff Pashnick
Prehistoric Europe experienced a marked cultural and economic shift around 4000 years ago, when the established Neolithic agriculture-based economy was replaced by herding-pastoralist industry. In recent years new data about the genetic structure of human communities living during this transition period began to emerge. At the same time, the genetic identities of the Eneolithic and Early Bronze Age (EBA) inhabitants from a prehistoric cultural crossroad in western North Pontic steppe region remain understudied...
February 2, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28123176/axial-spondylometaphyseal-dysplasia-is-also-caused-by-nek1-mutations
#14
Zheng Wang, Eva Horemuzova, Aritoshi Iida, Long Guo, Ying Liu, Naomichi Matsumoto, Gen Nishimura, Ann Nordgren, Noriko Miyake, Emma Tham, Giedre Grigelioniene, Shiro Ikegawa
Axial spondylometaphyseal dysplasia (axial SMD) is a unique form of SMD characterized by dysplasia of axial skeleton and retinal dystrophy. Recently, C21orf2 has been identified as the first disease gene for axial SMD; however, the presence of genetic heterogeneity is known. In this study, we identified NEK1 as the second disease gene for axial SMD. By whole-exome sequencing in a patient with axial SMD, we identified compound heterozygous mutations of NEK1, c.3107C>G (p.S1036*) and c.3830A>C (p.D1277A), which co-segregated in the family...
January 26, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28123175/a-novel-mutation-in-taz-causes-mitochondrial-respiratory-chain-disorder-without-cardiomyopathy
#15
Nurun N Borna, Yoshihito Kishita, Kaori Ishikawa, Kazuto Nakada, Jun-Ichi Hayashi, Yoshimi Tokuzawa, Masakazu Kohda, Hiromi Nyuzuki, Yzumi Yamashita-Sugahara, Takashi Nasu, Atsuhito Takeda, Kei Murayama, Akira Ohtake, Yasushi Okazaki
Tafazzin, encoded by the TAZ gene, is a mitochondrial membrane-associated protein that remodels cardiolipin (CL), an important mitochondrial phospholipid. TAZ mutations are associated with Barth syndrome (BTHS). BTHS is an X-linked multisystemic disorder affecting usually male patients. Through sequence analysis of TAZ, we found one novel mutation c.39_60del p.(Pro14Alafs*19) by whole-exome sequencing and a reported missense mutation c.280C>T p.(Arg94Cys) by Sanger sequencing in two male patients (Pt1 and Pt2)...
January 26, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28123174/new-diagnosis-of-atypical-ataxia-telangiectasia-in-a-17-year-old-boy-with-t-cell-acute-lymphoblastic-leukemia-and-a-novel-atm-mutation
#16
Jasmin Roohi, Jennifer Crowe, Denis Loredan, Kwame Anyane-Yeboa, Mahesh M Mansukhani, Lenore Omesi, Jennifer Levine, Anya Revah Politi, Shan Zha
Ataxia-telangiectasia (A-T) is an autosomal recessive chromosome breakage disorder caused by mutations in the ATM gene. Typically, it presents in early childhood with progressive cerebellar dysfunction along with immunodeficiency and oculocutaneous telangiectasia. An increased risk of malignancy is also associated with the syndrome and, rarely, may be the presenting feature in small children. We describe a 17-year-old boy with slurred speech, mild motor delays and learning disability diagnosed with atypical A-T in the setting of T-cell acute lymphoblastic leukemia...
January 26, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28100913/genome-wide-association-study-using-the-ethnicity-specific-japonica-array-identification-of-new-susceptibility-loci-for-cold-medicine-related-stevens-johnson-syndrome-with-severe-ocular-complications
#17
Mayumi Ueta, Hiromi Sawai, Ryosei Shingaki, Yusuke Kawai, Chie Sotozono, Kaname Kojima, Kyung-Chul Yoon, Mee Kum Kim, Kyoung Yul Seo, Choun-Ki Joo, Masao Nagasaki, Shigeru Kinoshita, Katsushi Tokunaga
A genome-wide association study (GWAS) for cold medicine-related Stevens-Johnson syndrome (CM-SJS) with severe ocular complications (SOC) was performed in a Japanese population. A recently developed ethnicity-specific array with genome-wide imputation that was based on the whole-genome sequences of 1070 unrelated Japanese individuals was used. Validation analysis with additional samples from Japanese individuals and replication analysis using samples from Korean individuals identified two new susceptibility loci on chromosomes 15 and 16...
January 19, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28100912/cryptic-splice-activation-but-not-exon-skipping-is-observed-in-minigene-assays-of-dystrophin-c-9361-1g-a-mutation-identified-by-ngs
#18
Emma Tabe Eko Niba, Atsushi Nishida, Van Khanh Tran, Dung Chi Vu, Masaaki Matsumoto, Hiroyuki Awano, Tomoko Lee, Yasuhiro Takeshima, Hisahide Nishio, Masafumi Matsuo
Next-generation sequencing (NGS) discloses nucleotide changes in the genome. Mutations at splicing regulatory elements are expected to cause splicing errors, such as exon skipping, cryptic splice site activation, partial exon loss or intron retention. In dystrophinopathy patients, prediction of splicing outcomes is essential to determine the phenotype: either severe Duchenne or mild Becker muscular dystrophy, based on the reading frame rule. In a Vietnamese patient, NGS identified a c.9361+1G>A mutation in the dystrophin gene and an additional DNA variation of A>G at +117 bases in intron 64...
January 19, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28100911/variants-on-chromosome-4q21-near-pkd2-and-siblings-are-associated-with-dental-caries
#19
Scott Eckert, Eleanor Feingold, Margaret Cooper, Michael M Vanyukov, Brion S Maher, Rebecca L Slayton, Marcia C Willing, Steven E Reis, Daniel W McNeil, Richard J Crout, Robert J Weyant, Steven M Levy, Alexandre R Vieira, Mary L Marazita, John R Shaffer
A recent genome-wide association study (GWAS) for dental caries nominated the chromosomal region 4q21 near ABCG2, PKD2 and the SIBLING (small integrin-binding ligand N-linked glycoprotein) gene family. In this investigation, we followed up and fine-mapped this region using a tag-SNP (single-nucleotide polymorphism) approach in 13 age- and race-stratified samples from 6 independent studies (N=4089). Participants were assessed for dental caries via intraoral examination and 49 tag-SNPs were genotyped capturing much of the variation in the 4q21 locus...
January 19, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28100910/a-novel-sequence-variant-in-sfrp4-causing-pyle-disease
#20
Chelna Galada, Hitesh Shah, Anju Shukla, Katta M Girisha
Pyle disease (PYL) is an extremely rare disorder of irregular development of long bone. Recently, homozygous mutations in secreted frizzled-related protein 4 gene (SFRP4) gene were found to underlie this condition. Sequencing of coding regions of SFRP4 gene from an 11-year-old female with PYL was performed. A novel homozygous nonsense variant, c.183C>G (p.Y61*) was observed. Segregation analysis in the patient revealed a germline mutation, resulting in reduced protein formation. This is the second report from a fourth affected family with a SFRP4 mutation causing PYL disease...
January 19, 2017: Journal of Human Genetics
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