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https://www.readbyqxmd.com/read/29157198/independent-impacts-of-aging-on-mitochondrial-dna-quantity-and-quality-in-humans
#1
Ruoyu Zhang, Yiqin Wang, Kaixiong Ye, Martin Picard, Zhenglong Gu
BACKGROUND: The accumulation of mitochondrial DNA (mtDNA) mutations, and the reduction of mtDNA copy number, both disrupt mitochondrial energetics, and may contribute to aging and age-associated phenotypes. However, there are few genetic and epidemiological studies on the spectra of blood mtDNA heteroplasmies, and the distribution of mtDNA copy numbers in different age groups and their impact on age-related phenotypes. In this work, we used whole-genome sequencing data of isolated peripheral blood mononuclear cells (PBMCs) from the UK10K project to investigate in parallel mtDNA heteroplasmy and copy number in 1511 women, between 17 and 85 years old, recruited in the TwinsUK cohorts...
November 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29148569/exome-sequence-analysis-and-follow-up-genotyping-implicates-rare-ulk1-variants-to-be-involved-in-susceptibility-to-schizophrenia
#2
Mariam M Al Eissa, Alessia Fiorentino, Sally I Sharp, Niamh L O'Brien, Kate Wolfe, Giovanni Giaroli, David Curtis, Nicholas J Bass, Andrew McQuillin
Schizophrenia (SCZ) is a severe, highly heritable psychiatric disorder. Elucidation of the genetic architecture of the disorder will facilitate greater understanding of the altered underlying neurobiological mechanisms. The aim of this study was to identify likely aetiological variants in subjects affected with SCZ. Exome sequence data from a SCZ cas-control sample from Sweden was analysed for likely aetiological variants using a weighted burden test. Suggestive evidence implicated the UNC-51-like kinase (ULK1) gene, and it was observed that four rare variants that were more common in the Swedish SCZ cases were also more common in UK10K SCZ cases, as compared to obesity cases...
November 17, 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/29107289/disruption-of-the-homeodomain-transcription-factor-orthopedia-homeobox-otp-is-associated-with-obesity-and-anxiety
#3
Lee Moir, Elena G Bochukova, Rebecca Dumbell, Gareth Banks, Rasneer S Bains, Patrick M Nolan, Cheryl Scudamore, Michelle Simon, Kimberly A Watson, Julia Keogh, Elana Henning, Audrey Hendricks, Stephen O'Rahilly, Inês Barroso, Adrienne E Sullivan, David C Bersten, Murray L Whitelaw, Susan Kirsch, Elizabeth Bentley, I Sadaf Farooqi, Roger D Cox
OBJECTIVE: Genetic studies in obese rodents and humans can provide novel insights into the mechanisms involved in energy homeostasis. METHODS: In this study, we genetically mapped the chromosomal region underlying the development of severe obesity in a mouse line identified as part of a dominant N-ethyl-N-nitrosourea (ENU) mutagenesis screen. We characterized the metabolic and behavioral phenotype of obese mutant mice and examined changes in hypothalamic gene expression...
November 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/28905877/population-specific-genetic-variation-in-large-sequencing-data-sets-why-more-data-is-still-better
#4
Jeroen G J van Rooij, Mila Jhamai, Pascal P Arp, Stephan C A Nouwens, Marijn Verkerk, Albert Hofman, M Arfan Ikram, Annemieke J Verkerk, Joyce B J van Meurs, Fernando Rivadeneira, André G Uitterlinden, Robert Kraaij
We have generated a next-generation whole-exome sequencing data set of 2628 participants of the population-based Rotterdam Study cohort, comprising 669 737 single-nucleotide variants and 24 019 short insertions and deletions. Because of broad and deep longitudinal phenotyping of the Rotterdam Study, this data set permits extensive interpretation of genetic variants on a range of clinically relevant outcomes, and is accessible as a control data set. We show that next-generation sequencing data sets yield a large degree of population-specific variants, which are not captured by other available large sequencing efforts, being ExAC, ESP, 1000G, UK10K, GoNL and DECODE...
October 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28887542/genome-wide-analysis-of-health-related-biomarkers-in-the-uk-household-longitudinal-study-reveals-novel-associations
#5
Bram P Prins, Karoline B Kuchenbaecker, Yanchun Bao, Melissa Smart, Delilah Zabaneh, Ghazaleh Fatemifar, Jian'an Luan, Nick J Wareham, Robert A Scott, John R B Perry, Claudia Langenberg, Michaela Benzeval, Meena Kumari, Eleftheria Zeggini
Serum biomarker levels are associated with the risk of complex diseases. Here, we aimed to gain insights into the genetic architecture of biomarker traits which can reflect health status. We performed genome-wide association analyses for twenty serum biomarkers involved in organ function and reproductive health. 9,961 individuals from the UK Household Longitudinal Study were genotyped using the Illumina HumanCoreExome array and variants imputed to the 1000 Genomes Project and UK10K haplotypes. We establish a polygenic heritability for all biomarkers, confirm associations of fifty-four established loci, and identify five novel, replicating associations at genome-wide significance...
September 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28757204/low-frequency-synonymous-coding-variation-in-cyp2r1-has-large-effects-on-vitamin-d-levels-and-risk-of-multiple-sclerosis
#6
Despoina Manousaki, Tom Dudding, Simon Haworth, Yi-Hsiang Hsu, Ching-Ti Liu, Carolina Medina-Gómez, Trudy Voortman, Nathalie van der Velde, Håkan Melhus, Cassianne Robinson-Cohen, Diana L Cousminer, Maria Nethander, Liesbeth Vandenput, Raymond Noordam, Vincenzo Forgetta, Celia M T Greenwood, Mary L Biggs, Bruce M Psaty, Jerome I Rotter, Babette S Zemel, Jonathan A Mitchell, Bruce Taylor, Mattias Lorentzon, Magnus Karlsson, Vincent V W Jaddoe, Henning Tiemeier, Natalia Campos-Obando, Oscar H Franco, Andre G Utterlinden, Linda Broer, Natasja M van Schoor, Annelies C Ham, M Arfan Ikram, David Karasik, Renée de Mutsert, Frits R Rosendaal, Martin den Heijer, Thomas J Wang, Lars Lind, Eric S Orwoll, Dennis O Mook-Kanamori, Karl Michaëlsson, Bryan Kestenbaum, Claes Ohlsson, Dan Mellström, Lisette C P G M de Groot, Struan F A Grant, Douglas P Kiel, M Carola Zillikens, Fernando Rivadeneira, Stephen Sawcer, Nicholas J Timpson, J Brent Richards
Vitamin D insufficiency is common, correctable, and influenced by genetic factors, and it has been associated with risk of several diseases. We sought to identify low-frequency genetic variants that strongly increase the risk of vitamin D insufficiency and tested their effect on risk of multiple sclerosis, a disease influenced by low vitamin D concentrations. We used whole-genome sequencing data from 2,619 individuals through the UK10K program and deep-imputation data from 39,655 individuals genotyped genome-wide...
August 3, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28669402/seqspark-a-complete-analysis-tool-for-large-scale-rare-variant-association-studies-using-whole-genome-and-exome-sequence-data
#7
Di Zhang, Linhai Zhao, Biao Li, Zongxiao He, Gao T Wang, Dajiang J Liu, Suzanne M Leal
Massively parallel sequencing technologies provide great opportunities for discovering rare susceptibility variants involved in complex disease etiology via large-scale imputation and exome and whole-genome sequence-based association studies. Due to modest effect sizes, large sample sizes of tens to hundreds of thousands of individuals are required for adequately powered studies. Current analytical tools are obsolete when it comes to handling these large datasets. To facilitate the analysis of large-scale sequence-based studies, we developed SEQSpark which implements parallel processing based on Spark to increase the speed and efficiency of performing data quality control, annotation, and association analysis...
July 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28663568/rare-variant-analysis-of-human-and-rodent-obesity-genes-in-individuals-with-severe-childhood-obesity
#8
Audrey E Hendricks, Elena G Bochukova, Gaëlle Marenne, Julia M Keogh, Neli Atanassova, Rebecca Bounds, Eleanor Wheeler, Vanisha Mistry, Elana Henning, Antje Körner, Dawn Muddyman, Shane McCarthy, Anke Hinney, Johannes Hebebrand, Robert A Scott, Claudia Langenberg, Nick J Wareham, Praveen Surendran, Joanna M Howson, Adam S Butterworth, John Danesh, Børge G Nordestgaard, Sune F Nielsen, Shoaib Afzal, Sofia Papadia, Sofie Ashford, Sumedha Garg, Glenn L Millhauser, Rafael I Palomino, Alexandra Kwasniewska, Ioanna Tachmazidou, Stephen O'Rahilly, Eleftheria Zeggini, Inês Barroso, I Sadaf Farooqi
Obesity is a genetically heterogeneous disorder. Using targeted and whole-exome sequencing, we studied 32 human and 87 rodent obesity genes in 2,548 severely obese children and 1,117 controls. We identified 52 variants contributing to obesity in 2% of cases including multiple novel variants in GNAS, which were sometimes found with accelerated growth rather than short stature as described previously. Nominally significant associations were found for rare functional variants in BBS1, BBS9, GNAS, MKKS, CLOCK and ANGPTL6...
June 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28650482/the-contribution-of-rare-variants-to-risk-of-schizophrenia-in-individuals-with-and-without-intellectual-disability
#9
Tarjinder Singh, James T R Walters, Mandy Johnstone, David Curtis, Jaana Suvisaari, Minna Torniainen, Elliott Rees, Conrad Iyegbe, Douglas Blackwood, Andrew M McIntosh, Georg Kirov, Daniel Geschwind, Robin M Murray, Marta Di Forti, Elvira Bramon, Michael Gandal, Christina M Hultman, Pamela Sklar, Aarno Palotie, Patrick F Sullivan, Michael C O'Donovan, Michael J Owen, Jeffrey C Barrett
By performing a meta-analysis of rare coding variants in whole-exome sequences from 4,133 schizophrenia cases and 9,274 controls, de novo mutations in 1,077 family trios, and copy number variants from 6,882 cases and 11,255 controls, we show that individuals with schizophrenia carry a significant burden of rare, damaging variants in 3,488 genes previously identified as having a near-complete depletion of loss-of-function variants. In patients with schizophrenia who also have intellectual disability, this burden is concentrated in risk genes associated with neurodevelopmental disorders...
August 2017: Nature Genetics
https://www.readbyqxmd.com/read/28643794/enrichment-of-low-frequency-functional-variants-revealed-by-whole-genome-sequencing-of-multiple-isolated-european-populations
#10
Yali Xue, Massimo Mezzavilla, Marc Haber, Shane McCarthy, Yuan Chen, Vagheesh Narasimhan, Arthur Gilly, Qasim Ayub, Vincenza Colonna, Lorraine Southam, Christopher Finan, Andrea Massaia, Himanshu Chheda, Priit Palta, Graham Ritchie, Jennifer Asimit, George Dedoussis, Paolo Gasparini, Aarno Palotie, Samuli Ripatti, Nicole Soranzo, Daniela Toniolo, James F Wilson, Richard Durbin, Chris Tyler-Smith, Eleftheria Zeggini
The genetic features of isolated populations can boost power in complex-trait association studies, and an in-depth understanding of how their genetic variation has been shaped by their demographic history can help leverage these advantageous characteristics. Here, we perform a comprehensive investigation using 3,059 newly generated low-depth whole-genome sequences from eight European isolates and two matched general populations, together with published data from the 1000 Genomes Project and UK10K. Sequencing data give deeper and richer insights into population demography and genetic characteristics than genotype-chip data, distinguishing related populations more effectively and allowing their functional variants to be studied more fully...
June 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28560825/phredem-a-phred-score-informed-genotype-calling-approach-for-next-generation-sequencing-studies
#11
Peizhou Liao, Glen A Satten, Yi-Juan Hu
A fundamental challenge in analyzing next-generation sequencing (NGS) data is to determine an individual's genotype accurately, as the accuracy of the inferred genotype is essential to downstream analyses. Correctly estimating the base-calling error rate is critical to accurate genotype calls. Phred scores that accompany each call can be used to decide which calls are reliable. Some genotype callers, such as GATK and SAMtools, directly calculate the base-calling error rates from phred scores or recalibrated base quality scores...
July 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28552196/whole-genome-sequencing-coupled-to-imputation-discovers-genetic-signals-for-anthropometric-traits
#12
Ioanna Tachmazidou, Dániel Süveges, Josine L Min, Graham R S Ritchie, Julia Steinberg, Klaudia Walter, Valentina Iotchkova, Jeremy Schwartzentruber, Jie Huang, Yasin Memari, Shane McCarthy, Andrew A Crawford, Cristina Bombieri, Massimiliano Cocca, Aliki-Eleni Farmaki, Tom R Gaunt, Pekka Jousilahti, Marjolein N Kooijman, Benjamin Lehne, Giovanni Malerba, Satu Männistö, Angela Matchan, Carolina Medina-Gomez, Sarah J Metrustry, Abhishek Nag, Ioanna Ntalla, Lavinia Paternoster, Nigel W Rayner, Cinzia Sala, William R Scott, Hashem A Shihab, Lorraine Southam, Beate St Pourcain, Michela Traglia, Katerina Trajanoska, Gialuigi Zaza, Weihua Zhang, María S Artigas, Narinder Bansal, Marianne Benn, Zhongsheng Chen, Petr Danecek, Wei-Yu Lin, Adam Locke, Jian'an Luan, Alisa K Manning, Antonella Mulas, Carlo Sidore, Anne Tybjaerg-Hansen, Anette Varbo, Magdalena Zoledziewska, Chris Finan, Konstantinos Hatzikotoulas, Audrey E Hendricks, John P Kemp, Alireza Moayyeri, Kalliope Panoutsopoulou, Michal Szpak, Scott G Wilson, Michael Boehnke, Francesco Cucca, Emanuele Di Angelantonio, Claudia Langenberg, Cecilia Lindgren, Mark I McCarthy, Andrew P Morris, Børge G Nordestgaard, Robert A Scott, Martin D Tobin, Nicholas J Wareham, Paul Burton, John C Chambers, George Davey Smith, George Dedoussis, Janine F Felix, Oscar H Franco, Giovanni Gambaro, Paolo Gasparini, Christopher J Hammond, Albert Hofman, Vincent W V Jaddoe, Marcus Kleber, Jaspal S Kooner, Markus Perola, Caroline Relton, Susan M Ring, Fernando Rivadeneira, Veikko Salomaa, Timothy D Spector, Oliver Stegle, Daniela Toniolo, André G Uitterlinden, Inês Barroso, Celia M T Greenwood, John R B Perry, Brian R Walker, Adam S Butterworth, Yali Xue, Richard Durbin, Kerrin S Small, Nicole Soranzo, Nicholas J Timpson, Eleftheria Zeggini
Deep sequence-based imputation can enhance the discovery power of genome-wide association studies by assessing previously unexplored variation across the common- and low-frequency spectra. We applied a hybrid whole-genome sequencing (WGS) and deep imputation approach to examine the broader allelic architecture of 12 anthropometric traits associated with height, body mass, and fat distribution in up to 267,616 individuals. We report 106 genome-wide significant signals that have not been previously identified, including 9 low-frequency variants pointing to functional candidates...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28546572/corrigendum-mutations-in-the-histone-methyltransferase-gene-kmt2b-cause-complex-early-onset-dystonia
#13
Esther Meyer, Keren J Carss, Julia Rankin, John M E Nichols, Detelina Grozeva, Agnel P Joseph, Niccolo E Mencacci, Apostolos Papandreou, Joanne Ng, Serena Barral, Adeline Ngoh, Hilla Ben-Pazi, Michel A Willemsen, David Arkadir, Angela Barnicoat, Hagai Bergman, Sanjay Bhate, Amber Boys, Niklas Darin, Nicola Foulds, Nicholas Gutowski, Alison Hills, Henry Houlden, Jane A Hurst, Zvi Israel, Margaret Kaminska, Patricia Limousin, Daniel Lumsden, Shane McKee, Shibalik Misra, Shekeeb S Mohammed, Vasiliki Nakou, Joost Nicolai, Magnus Nilsson, Hardev Pall, Kathryn J Peall, Gregory B Peters, Prab Prabhakar, Miriam S Reuter, Patrick Rump, Reeval Segel, Margje Sinnema, Martin Smith, Peter Turnpenny, Susan M White, Dagmar Wieczorek, Sarah Wiethoff, Brian T Wilson, Gidon Winter, Christopher Wragg, Simon Pope, Simon J H Heales, Deborah Morrogh, Alan Pittman, Lucinda J Carr, Belen Perez-Dueñas, Jean-Pierre Lin, Andre Reis, William A Gahl, Camilo Toro, Kailash P Bhatia, Nicholas W Wood, Erik-Jan Kamsteeg, Wui K Chong, Paul Gissen, Maya Topf, Russell C Dale, Jonathan R Chubb, F Lucy Raymond, Manju A Kurian
No abstract text is available yet for this article.
May 26, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28493397/a-recurrent-de-novo-mutation-in-actg1-causes-isolated-ocular-coloboma
#14
Joe Rainger, Kathleen A Williamson, Dinesh C Soares, Julia Truch, Dominic Kurian, Gabriele Gillessen-Kaesbach, Anne Seawright, James Prendergast, Mihail Halachev, Ann Wheeler, Lynn McTeir, Andrew C Gill, Veronica van Heyningen, Megan G Davey, David R FitzPatrick
Ocular coloboma (OC) is a defect in optic fissure closure and is a common cause of severe congenital visual impairment. Bilateral OC is primarily genetically determined and shows marked locus heterogeneity. Whole-exome sequencing (WES) was used to analyze 12 trios (child affected with OC and both unaffected parents). This identified de novo mutations in 10 different genes in eight probands. Three of these genes encoded proteins associated with actin cytoskeleton dynamics: ACTG1, TWF1, and LCP1. Proband-only WES identified a second unrelated individual with isolated OC carrying the same ACTG1 allele, encoding p...
August 2017: Human Mutation
https://www.readbyqxmd.com/read/28472463/genome-wide-association-study-meta-analysis-for-quantitative-ultrasound-parameters-of-bone-identifies-five-novel-loci-for-broadband-ultrasound-attenuation
#15
Benjamin H Mullin, Jing Hua Zhao, Suzanne J Brown, John R B Perry, Jian'an Luan, Hou-Feng Zheng, Claudia Langenberg, Frank Dudbridge, Robert Scott, Nick J Wareham, Tim D Spector, J Brent Richards, John P Walsh, Scott G Wilson
Osteoporosis is a common and debilitating bone disease that is characterised by low bone mineral density, typically assessed using dual-energy X-ray absorptiometry. Quantitative ultrasound (QUS), commonly utilising the two parameters velocity of sound (VOS) and broadband ultrasound attenuation (BUA), is an alternative technology used to assess bone properties at peripheral skeletal sites. The genetic influence on the bone qualities assessed by QUS remains an under-studied area. We performed a comprehensive genome-wide association study (GWAS) including low-frequency variants (minor allele frequency ≥0...
July 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28349888/screening-for-familial-hypercholesterolaemia-in-childhood-avon-longitudinal-study-of-parents-and-children-alspac
#16
Marta Futema, Jackie A Cooper, Marietta Charakida, Christopher Boustred, Naveed Sattar, John Deanfield, Debbie A Lawlor, Nicholas J Timpson, Steve E Humphries, Aroon D Hingorani
BACKGROUND AND AIMS: Familial hypercholesterolaemia (FH) is an autosomal-dominant disease with frequency of 1/500 to 1/250 that leads to premature coronary heart disease. New approaches to identify FH mutation-carriers early are needed to prevent premature cardiac deaths. In a cross-sectional study of the Avon Longitudinal Study of Parents and Children (ALSPAC), we evaluated the biochemical thresholds for FH screening in childhood, and modelled a two-stage biochemical and sequencing screening strategy for FH detection...
May 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28176794/x-linked-primary-ciliary-dyskinesia-due-to-mutations-in-the-cytoplasmic-axonemal-dynein-assembly-factor-pih1d3
#17
Chiara Olcese, Mitali P Patel, Amelia Shoemark, Santeri Kiviluoto, Marie Legendre, Hywel J Williams, Cara K Vaughan, Jane Hayward, Alice Goldenberg, Richard D Emes, Mustafa M Munye, Laura Dyer, Thomas Cahill, Jeremy Bevillard, Corinne Gehrig, Michel Guipponi, Sandra Chantot, Philippe Duquesnoy, Lucie Thomas, Ludovic Jeanson, Bruno Copin, Aline Tamalet, Christel Thauvin-Robinet, Jean-François Papon, Antoine Garin, Isabelle Pin, Gabriella Vera, Paul Aurora, Mahmoud R Fassad, Lucy Jenkins, Christopher Boustred, Thomas Cullup, Mellisa Dixon, Alexandros Onoufriadis, Andrew Bush, Eddie M K Chung, Stylianos E Antonarakis, Michael R Loebinger, Robert Wilson, Miguel Armengot, Estelle Escudier, Claire Hogg, Serge Amselem, Zhaoxia Sun, Lucia Bartoloni, Jean-Louis Blouin, Hannah M Mitchison
By moving essential body fluids and molecules, motile cilia and flagella govern respiratory mucociliary clearance, laterality determination and the transport of gametes and cerebrospinal fluid. Primary ciliary dyskinesia (PCD) is an autosomal recessive disorder frequently caused by non-assembly of dynein arm motors into cilia and flagella axonemes. Before their import into cilia and flagella, multi-subunit axonemal dynein arms are thought to be stabilized and pre-assembled in the cytoplasm through a DNAAF2-DNAAF4-HSP90 complex akin to the HSP90 co-chaperone R2TP complex...
February 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/28165464/genome-wide-association-analysis-implicates-dysregulation-of-immunity-genes-in-chronic-lymphocytic-leukaemia
#18
Philip J Law, Sonja I Berndt, Helen E Speedy, Nicola J Camp, Georgina P Sava, Christine F Skibola, Amy Holroyd, Vijai Joseph, Nicola J Sunter, Alexandra Nieters, Silvia Bea, Alain Monnereau, David Martin-Garcia, Lynn R Goldin, Guillem Clot, Lauren R Teras, Inés Quintela, Brenda M Birmann, Sandrine Jayne, Wendy Cozen, Aneela Majid, Karin E Smedby, Qing Lan, Claire Dearden, Angela R Brooks-Wilson, Andrew G Hall, Mark P Purdue, Tryfonia Mainou-Fowler, Claire M Vajdic, Graham H Jackson, Pierluigi Cocco, Helen Marr, Yawei Zhang, Tongzhang Zheng, Graham G Giles, Charles Lawrence, Timothy G Call, Mark Liebow, Mads Melbye, Bengt Glimelius, Larry Mansouri, Martha Glenn, Karen Curtin, W Ryan Diver, Brian K Link, Lucia Conde, Paige M Bracci, Elizabeth A Holly, Rebecca D Jackson, Lesley F Tinker, Yolanda Benavente, Paolo Boffetta, Paul Brennan, Marc Maynadie, James McKay, Demetrius Albanes, Stephanie Weinstein, Zhaoming Wang, Neil E Caporaso, Lindsay M Morton, Richard K Severson, Elio Riboli, Paolo Vineis, Roel C H Vermeulen, Melissa C Southey, Roger L Milne, Jacqueline Clavel, Sabine Topka, John J Spinelli, Peter Kraft, Maria Grazia Ennas, Geoffrey Summerfield, Giovanni M Ferri, Robert J Harris, Lucia Miligi, Andrew R Pettitt, Kari E North, David J Allsup, Joseph F Fraumeni, James R Bailey, Kenneth Offit, Guy Pratt, Henrik Hjalgrim, Chris Pepper, Stephen J Chanock, Chris Fegan, Richard Rosenquist, Silvia de Sanjose, Angel Carracedo, Martin J S Dyer, Daniel Catovsky, Elias Campo, James R Cerhan, James M Allan, Nathanial Rothman, Richard Houlston, Susan Slager
Several chronic lymphocytic leukaemia (CLL) susceptibility loci have been reported; however, much of the heritable risk remains unidentified. Here we perform a meta-analysis of six genome-wide association studies, imputed using a merged reference panel of 1,000 Genomes and UK10K data, totalling 6,200 cases and 17,598 controls after replication. We identify nine risk loci at 1p36.11 (rs34676223, P=5.04 × 10(-13)), 1q42.13 (rs41271473, P=1.06 × 10(-10)), 4q24 (rs71597109, P=1.37 × 10(-10)), 4q35.1 (rs57214277, P=3...
February 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/28151491/clinical-and-molecular-consequences-of-disease-associated-de-novo-mutations-in-satb2
#19
Hemant Bengani, Mark Handley, Mohsan Alvi, Rita Ibitoye, Melissa Lees, Sally Ann Lynch, Wayne Lam, Madeleine Fannemel, Ann Nordgren, H Malmgren, M Kvarnung, Sarju Mehta, Shane McKee, Margo Whiteford, Fiona Stewart, Fiona Connell, Jill Clayton-Smith, Sahar Mansour, Shehla Mohammed, Alan Fryer, Jenny Morton, Detelina Grozeva, Tara Asam, David Moore, Alejandro Sifrim, Jeremy McRae, Matthew E Hurles, Helen V Firth, F Lucy Raymond, Usha Kini, Christoffer Nellåker, Ddd Study, David R FitzPatrick
PURPOSE: To characterize features associated with de novo mutations affecting SATB2 function in individuals ascertained on the basis of intellectual disability. METHODS: Twenty previously unreported individuals with 19 different SATB2 mutations (11 loss-of-function and 8 missense variants) were studied. Fibroblasts were used to measure mutant protein production. Subcellular localization and mobility of wild-type and mutant SATB2 were assessed using fluorescently tagged protein...
August 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28145424/whole-genome-view-of-the-consequences-of-a-population-bottleneck-using-2926-genome-sequences-from-finland-and-united-kingdom
#20
Himanshu Chheda, Priit Palta, Matti Pirinen, Shane McCarthy, Klaudia Walter, Seppo Koskinen, Veikko Salomaa, Mark Daly, Richard Durbin, Aarno Palotie, Tero Aittokallio, Samuli Ripatti
Isolated populations with enrichment of variants due to recent population bottlenecks provide a powerful resource for identifying disease-associated genetic variants and genes. As a model of an isolate population, we sequenced the genomes of 1463 Finnish individuals as part of the Sequencing Initiative Suomi (SISu) Project. We compared the genomic profiles of the 1463 Finns to a sample of 1463 British individuals that were sequenced in parallel as part of the UK10K Project. Whereas there were no major differences in the allele frequency of common variants, a significant depletion of variants in the rare frequency spectrum was observed in Finns when comparing the two populations...
April 2017: European Journal of Human Genetics: EJHG
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