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Human Genetics

Sara Lindström, Marine Germain, Marta Crous-Bou, Erin N Smith, Pierre-Emmanuel Morange, Astrid van Hylckama Vlieg, Hugoline G de Haan, Daniel Chasman, Paul Ridker, Jennifer Brody, Mariza de Andrade, John A Heit, Weihong Tang, Immaculata De Vivo, Francine Grodstein, Nicholas L Smith, David Tregouet, Christopher Kabrhel
The co-author name Immaculata DeVivo was incorrectly published. The correct name is given below.
May 19, 2018: Human Genetics
Mieke Wesdorp, Pia A M de Koning Gans, Margit Schraders, Jaap Oostrik, Martijn A Huynen, Hanka Venselaar, Andy J Beynon, Judith van Gaalen, Vitória Piai, Nicol Voermans, Michelle M van Rossum, Bas P Hartel, Stefan H Lelieveld, Laurens Wiel, Berit Verbist, Liselotte J Rotteveel, Marieke F van Dooren, Peter Lichtner, Henricus P M Kunst, Ilse Feenstra, Ronald J C Admiraal, Helger G Yntema, Lies H Hoefsloot, Ronald J E Pennings, Hannie Kremer
Unraveling the causes and pathomechanisms of progressive disorders is essential for the development of therapeutic strategies. Here, we identified heterozygous pathogenic missense variants of LMX1A in two families of Dutch origin with progressive nonsyndromic hearing impairment (HI), using whole exome sequencing. One variant, c.721G > C (p.Val241Leu), occurred de novo and is predicted to affect the homeodomain of LMX1A, which is essential for DNA binding. The second variant, c.290G > C (p.Cys97Ser), predicted to affect a zinc-binding residue of the second LIM domain that is involved in protein-protein interactions...
May 12, 2018: Human Genetics
M Krall, S Htun, D Anand, D Hart, S A Lachke, A M Slavotinek
The authors noticed that Fig. 5A and B aspect ratios appeared sub-optimal in the online published version. This has now been changed.
May 11, 2018: Human Genetics
Lot Snijders Blok, Susan M Hiatt, Kevin M Bowling, Jeremy W Prokop, Krysta L Engel, J Nicholas Cochran, E Martina Bebin, Emilia K Bijlsma, Claudia A L Ruivenkamp, Paulien Terhal, Marleen E H Simon, Rosemarie Smith, Jane A Hurst, Heather McLaughlin, Richard Person, Amy Crunk, Michael F Wangler, Haley Streff, Joseph D Symonds, Sameer M Zuberi, Katherine S Elliott, Victoria R Sanders, Abigail Masunga, Robert J Hopkin, Holly A Dubbs, Xilma R Ortiz-Gonzalez, Rolph Pfundt, Han G Brunner, Simon E Fisher, Tjitske Kleefstra, Gregory M Cooper
Many genetic causes of developmental delay and/or intellectual disability (DD/ID) are extremely rare, and robust discovery of these requires both large-scale DNA sequencing and data sharing. Here we describe a GeneMatcher collaboration which led to a cohort of 13 affected individuals harboring protein-altering variants, 11 of which are de novo, in MED13; the only inherited variant was transmitted to an affected child from an affected mother. All patients had intellectual disability and/or developmental delays, including speech delays or disorders...
May 8, 2018: Human Genetics
Lisa Neuhäusler, Anna Summerer, David N Cooper, Victor-F Mautner, Hildegard Kehrer-Sawatzki
Neurofibromatosis type 1 (NF1) is caused, in 4.7-11% of cases, by large deletions encompassing the NF1 gene and its flanking regions within 17q11.2. Different types of large NF1 deletion occur which are distinguishable by their breakpoint location and underlying mutational mechanism. Most common are the type-1 NF1 deletions of 1.4 Mb which exhibit recurrent breakpoints caused by nonallelic homologous recombination (NAHR), also termed unequal crossover. Here, we analyzed 37 unrelated families of patients with de novo type-1 NF1 deletions by means of short tandem repeat (STR) profiling to determine the parental origin of the deletions...
May 5, 2018: Human Genetics
Andrew J Mowat, Michael Crompton, Joanna L Ziff, Christopher P Aldren, Jeremy A Lavy, Shakeel R Saeed, Sally J Dawson
Otosclerosis is a common form of hearing loss which typically presents in young adults. The disease has a familial, monogenic form and a non-familial form with a more complex aetiology. A previous genome wide association study identified evidence that variants within RELN are associated with the condition. Other genes in which an association has been reported include BMP2, COL1A1, FGF2, PPP2R5B and TGFB1. However, follow up studies have often failed to replicate initial positive results. The aim of this study was to establish if an association exists between eight single nucleotide polymorphisms (SNPs) in these six previously implicated genes and otosclerosis in a British case-control cohort (n = 748)...
May 4, 2018: Human Genetics
M Krall, S Htun, D Anand, D Hart, S A Lachke, A M Slavotinek
The Forkhead box E3 (FOXE3) gene encodes a transcription factor with a forkhead/winged helix domain that is critical for development of the lens and anterior segment of the eye. Monoallelic and biallelic deleterious sequence variants in FOXE3 cause aphakia, cataracts, sclerocornea and microphthalmia in humans. We used clustered regularly interspaced short palindromic repeats/Cas9 injections to target the foxe3 transcript in zebrafish in order to create an experimental model of loss of function for this gene...
April 30, 2018: Human Genetics
Todd Lencz, Jin Yu, Cameron Palmer, Shai Carmi, Danny Ben-Avraham, Nir Barzilai, Susan Bressman, Ariel Darvasi, Judy H Cho, Lorraine N Clark, Zeynep H Gümüş, Vijai Joseph, Robert Klein, Steven Lipkin, Kenneth Offit, Harry Ostrer, Laurie J Ozelius, Inga Peter, Gil Atzmon, Itsik Pe'er
While increasingly large reference panels for genome-wide imputation have been recently made available, the degree to which imputation accuracy can be enhanced by population-specific reference panels remains an open question. Here, we sequenced at full-depth (≥ 30×), across two platforms (Illumina X Ten and Complete Genomics, Inc.), a moderately large (n = 738) cohort of samples drawn from the Ashkenazi Jewish population. We developed a series of quality control steps to optimize sensitivity, specificity, and comprehensiveness of variant calls in the reference panel, and then tested the accuracy of imputation against target cohorts drawn from the same population...
April 28, 2018: Human Genetics
Joshi Stephen, Sheela Nampoothiri, Aditi Banerjee, Nathanial J Tolman, Josef Martin Penninger, Ullrich Elling, Chukwuma A Agu, John D Burke, Kalpana Devadathan, Rajesh Kannan, Yan Huang, Peter J Steinbach, Susan A Martinis, William A Gahl, May Christine V Malicdan
Progressive microcephaly and neurodegeneration are genetically heterogenous conditions, largely associated with genes that are essential for the survival of neurons. In this study, we interrogate the genetic etiology of two siblings from a non-consanguineous family with severe early onset of neurological manifestations. Whole exome sequencing identified novel compound heterozygous mutations in VARS that segregated with the proband: a missense (c.3192G>A; p.Met1064Ile) and a splice site mutation (c.1577-2A>G)...
April 24, 2018: Human Genetics
Ezgi Kucukkilic, Keeley Brookes, Imelda Barber, Tamar Guetta-Baranes, Kevin Morgan, Edward J Hollox
Single nucleotide variants (SNVs) within and surrounding the complement receptor 1 (CR1) gene show some of the strongest genome-wide association signals with late-onset Alzheimer's disease. Some studies have suggested that this association signal is due to a duplication allele (CR1-B) of a low copy repeat (LCR) within the CR1 gene, which increases the number of complement C3b/C4b-binding sites in the mature receptor. In this study, we develop a triplex paralogue ratio test assay for CR1 LCR copy number allowing large numbers of samples to be typed with a limited amount of DNA...
April 19, 2018: Human Genetics
Candelaria Vergara, Margaret M Parker, Liliana Franco, Michael H Cho, Ana V Valencia-Duarte, Terri H Beaty, Priya Duggal
Genotype imputation estimates unobserved genotypes from genome-wide makers, to increase genome coverage and power for genome-wide association studies. Imputation has been successful for European ancestry populations in which very large reference panels are available. Smaller subsets of African descent populations are available in 1000 Genomes (1000G), the Consortium on Asthma among African ancestry Populations in the Americas (CAAPA) and the Haplotype Reference Consortium (HRC). We compared the performance of these reference panels when imputing variation in 3747 African Americans (AA) from two cohorts (HCV and COPDGene) genotyped using Illumina Omni microarrays...
April 10, 2018: Human Genetics
Hessa S Alsaif, Arif O Khan, Nisha Patel, Hisham Alkuraya, Mais Hashem, Firdous Abdulwahab, Niema Ibrahim, Mohammed A Aldahmesh, Fowzan S Alkuraya
Primary congenital glaucoma is a trabecular meshwork dysgenesis with resultant increased intraocular pressure and ocular damage. CYP1B1 mutations remain the most common identifiable genetic cause. However, important questions about the penetrance of CYP1B1-related congenital glaucoma remain unanswered. Furthermore, mutations in other genes have been described although their exact contribution and potential genetic interaction, if any, with CYP1B1 mutations are not fully explored. In this study, we employed modern genomic approaches to re-examine CYP1B1-related congenital glaucoma...
March 19, 2018: Human Genetics
Magalie S Leduc, Marianne Mcguire, Suneeta Madan-Khetarpal, Damara Ortiz, Susan Hayflick, Kory Keller, Christine M Eng, Yaping Yang, Weimin Bi
PRR12 encodes a proline-rich protein nuclear factor suspected to be involved in neural development. Its nuclear expression in fetal brains and in the vision system supports its role in brain and eye development more specifically. However, its function and potential role in human disease has not been determined. Recently, a de novo t(10;19) (q22.3;q13.33) translocation disrupting the PRR12 gene was detected in a girl with intellectual disability and neuropsychiatric alterations. Here we report on three unrelated patients with heterozygous de novo apparent loss-of-function mutations in PRR12 detected by clinical whole exome sequencing: c...
March 19, 2018: Human Genetics
Wu Li, Jie Sun, Jie Ling, Jiada Li, Chufeng He, Yalan Liu, Hongsheng Chen, Meichao Men, Zhijie Niu, Yuyuan Deng, Meng Li, Taoxi Li, Jie Wen, Shushan Sang, Haibo Li, Zhengqing Wan, Elodie M Richard, Prem Chapagain, Denise Yan, Xue Zhong Liu, Lingyun Mei, Yong Feng
Autosomal dominant nonsyndromic hearing loss (ADNSHL) is a highly genetically heterogeneous disorder. Up to date only approximately 37 ADNSHL-causing genes have been identified. The goal of this study was to determine the causative gene in a five-generation Chinese family with ADNSHL. A Chinese family was ascertained. Simultaneously, two affected individuals and one normal hearing control from the family were analyzed by whole exome capture sequencing. To assess the functional effect of the identified variant, in-vitro studies were performed...
April 2018: Human Genetics
Hao Wang, Lele Zhang, Nan Wang, Hui Zhu, Bing Han, Feng Sun, Haijun Yao, Qiang Zhang, Wenjiao Zhu, Tong Cheng, Kaixiang Cheng, Yang Liu, Shuangxia Zhao, Huaidong Song, Jie Qiao
Disorders of sexual development (DSD) are rare congenital conditions in which chromosomal, gonadal, or anatomical sex is atypical. Currently, less than 20% of patients receive an accurate genetic diagnosis. Targeted next-generation sequencing, consisting of 33 candidate genes and 47 genes involved in sexual differentiation and development, was performed on 70 46, XY DSD patients. Functional assays were performed to evaluate the expression and transcriptional activity of one reported and nine novel mutations of NR5A1...
March 2018: Human Genetics
Xiang-He Meng, Hui Shen, Xiang-Ding Chen, Hong-Mei Xiao, Hong-Wen Deng
Genome-wide association studies (GWAS) have successfully identified numerous genetic variants associated with diverse complex phenotypes and diseases, and provided tremendous opportunities for further analyses using summary association statistics. Recently, Pickrell et al. developed a robust method for causal inference using independent putative causal SNPs. However, this method may fail to infer the causal relationship between two phenotypes when only a limited number of independent putative causal SNPs identified...
March 2018: Human Genetics
Lisbeth Tranebjærg, Nicola Strenzke, Sture Lindholm, Nanna D Rendtorff, Hanne Poulsen, Himanshu Khandelia, Wojciech Kopec, Troels J Brünnich Lyngbye, Christian Hamel, Cecile Delettre, Beatrice Bocquet, Michael Bille, Hanne H Owen, Toke Bek, Hanne Jensen, Karen Østergaard, Claes Möller, Linda Luxon, Lucinda Carr, Louise Wilson, Kaukab Rajput, Tony Sirimanna, Katherine Harrop-Griffiths, Shamima Rahman, Barbara Vona, Julia Doll, Thomas Haaf, Oliver Bartsch, Hendrik Rosewich, Tobias Moser, Maria Bitner-Glindzicz
The following information was inadvertently omitted in the original publication.
March 2018: Human Genetics
Leslie E W LaConte, Vrushali Chavan, Abdallah F Elias, Cynthia Hudson, Corbin Schwanke, Katie Styren, Jonathan Shoof, Fernando Kok, Sarika Srivastava, Konark Mukherjee
Deletion and truncation mutations in the X-linked gene CASK are associated with severe intellectual disability (ID), microcephaly and pontine and cerebellar hypoplasia in girls (MICPCH). The molecular origin of CASK-linked MICPCH is presumed to be due to disruption of the CASK-Tbr-1 interaction. This hypothesis, however, has not been directly tested. Missense variants in CASK are typically asymptomatic in girls. We report three severely affected girls with heterozygous CASK missense mutations (M519T (2), G659D (1)) who exhibit ID, microcephaly, and hindbrain hypoplasia...
March 2018: Human Genetics
George Kanoungi, Michael Nothnagel
Complex diseases are frequently modeled as following an additive model that excludes both intra- and inter-locus interaction, while at the same time reports on non-additive biological structures are ample, prominently featuring numerous metabolic and signaling pathways. Using extensive forward population simulations, we explored the impact of three basic pathway motifs on the relationship between epidemiological parameters, including disease prevalence, relative risk, sibling recurrence risk as well as causal variant number and allele frequency...
March 2018: Human Genetics
Chunyu Liu, Jessica L Fetterman, Poching Liu, Yan Luo, Martin G Larson, Ramachandran S Vasan, Jun Zhu, Daniel Levy
Increasing evidence implicates mitochondrial dysfunction in aging and age-related conditions. But little is known about the molecular basis for this connection. A possible cause may be mutations in the mitochondrial DNA (mtDNA), which are often heteroplasmic-the joint presence of different alleles at a single locus in the same individual. However, the involvement of mtDNA heteroplasmy in aging and age-related conditions has not been investigated thoroughly. We deep-sequenced the complete mtDNA genomes of 356 Framingham Heart Study participants (52% women, mean age 43, mean coverage 4570-fold), identified 2880 unique mutations and comprehensively annotated them by MITOMAP and PolyPhen-2...
March 2018: Human Genetics
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