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Molecular Genetics & Genomic Medicine

Carolien G F de Kovel, Eva H Brilstra, Marjan J A van Kempen, Ruben Van't Slot, Isaac J Nijman, Zaid Afawi, Peter De Jonghe, Tania Djémié, Renzo Guerrini, Katia Hardies, Ingo Helbig, Rik Hendrickx, Moine Kanaan, Uri Kramer, Anna-Elina E Lehesjoki, Johannes R Lemke, Carla Marini, Davide Mei, Rikke S Møller, Manuela Pendziwiat, Hannah Stamberger, Arvid Suls, Sarah Weckhuysen, Bobby P C Koeleman
BACKGROUND: Many genes are candidates for involvement in epileptic encephalopathy (EE) because one or a few possibly pathogenic variants have been found in patients, but insufficient genetic or functional evidence exists for a definite annotation. METHODS: To increase the number of validated EE genes, we sequenced 26 known and 351 candidate genes for EE in 360 patients. Variants in 25 genes known to be involved in EE or related phenotypes were followed up in 41 patients...
September 2016: Molecular Genetics & Genomic Medicine
Martina Dreßen, Harald Lahm, Armin Lahm, Klaudia Wolf, Stefanie Doppler, Marcus-André Deutsch, Julie Cleuziou, Jelena Pabst von Ohain, Patric Schön, Peter Ewert, Ivan Malcic, Rüdiger Lange, Markus Krane
BACKGROUND: The Holt-Oram syndrome (HOS) is an autosomal dominant disorder affecting 1/100.000 live births. It is defined by upper limb anomalies and congenital heart defects with variable severity. We describe a dramatic phenotype of a male, 15-month-old patient being investigated for strict diagnostic criteria of HOS. METHODS AND RESULTS: Genetic analysis revealed a so far unpublished TBX5 mutation, which occurs de novo in the patient with healthy parents. TBX5 belongs to the large family of T-box transcription factors playing major roles in morphogenesis and cell-type specification...
September 2016: Molecular Genetics & Genomic Medicine
Daniel R Jacobson, Alice A Alexander, Clement Tagoe, W T Garvey, Scott M Williams, Sara Tishkoff, David Modiano, Sodiomon B Sirima, Issa Kalidi, Amadou Toure, Joel N Buxbaum
BACKGROUND: Transthyretin (TTR) pV142I (rs76992529-A) is one of the 113 variants in the human TTR gene associated with systemic amyloidosis. It results from a G to A transition at a CG dinucleotide in the codon for amino acid 122 of the mature protein (TTR V122I). The allele frequency is 0.0173 in African Americans. METHODS: PCR-based assays to genotype 2767 DNA samples obtained from participants in genetic studies from various African populations supplemented with sequencing data from 529 samples within the 1000 Genomes Project...
September 2016: Molecular Genetics & Genomic Medicine
Maria T Acosta, James Swanson, Annamarie Stehli, Brooke S G Molina, Ariel F Martinez, Mauricio Arcos-Burgos, Maximilian Muenke
BACKGROUND: ADHD is the most common neuropsychiatric condition affecting individuals of all ages. Long-term outcomes of affected individuals and association with severe comorbidities as SUD or conduct disorders are the main concern. Genetic associations have been extensively described. Multiple studies show that intronic variants harbored in the ADGRL3 (LPHN3) gene are associated with ADHD, especially associated with poor outcomes. METHODS: In this study, we evaluated this association in the Multimodal Treatment Study of children with ADHD (MTA), initiated as a 14-month randomized clinical trial of 579 children diagnosed with DSM-IV ADHD-Combined Type (ADHD-C), that transitioned to a 16-year prospective observational follow-up, and 289 classmates added at the 2-year assessment to serve as a local normative comparison group (LNCG)...
September 2016: Molecular Genetics & Genomic Medicine
Ola Abdelhadi, Daniela Iancu, Mehmet Tekman, Horia Stanescu, Detlef Bockenhauer, Robert Kleta
BACKGROUND: EAST syndrome is an autosomal recessive disorder caused by loss-of-function mutations in the gene KCNJ10. Among the 14 pathogenic mutations described so far, the p.R65P mutation stands out as the most frequent one and is particularly associated with patients of Pakistani origin. As a result we aimed to establish the existence of a potential founder effect in the Pakistani population. METHODS: To this end, we genotyped 12 patients from seven families and we compared disease haplotypes with ethnically matched control chromosomes...
September 2016: Molecular Genetics & Genomic Medicine
Roxana Daneshjou, Larisa H Cavallari, Peter E Weeke, Konrad J Karczewski, Katarzyna Drozda, Minoli A Perera, Julie A Johnson, Teri E Klein, Carlos D Bustamante, Dan M Roden, Christian Shaffer, Joshua C Denny, James L Zehnder, Russ B Altman
INTRODUCTION: African Americans have a higher incidence of venous thromboembolism (VTE) than European descent individuals. However, the typical genetic risk factors in populations of European descent are nearly absent in African Americans, and population-specific genetic factors influencing the higher VTE rate are not well characterized. METHODS: We performed a candidate gene analysis on an exome-sequenced African American family with recurrent VTE and identified a variant in Protein S (PROS1) V510M (rs138925964)...
September 2016: Molecular Genetics & Genomic Medicine
Alison Hamilton, Martine Tétreault, David A Dyment, Ruobing Zou, Kristin Kernohan, Michael T Geraghty, Taila Hartley, Kym M Boycott
The clinical translation of next-generation sequencing has created a paradigm shift in the diagnostic assessment of individuals with suspected rare genetic diseases. Whole-exome sequencing (WES) simultaneously examines the majority of the coding portion of the genome and is rapidly becoming accepted as an efficient alternative to clinical Sanger sequencing for diagnosing genetically heterogeneous disorders. Among reports of the clinical and diagnostic utility of WES, few studies to date have directly compared its concordance to Sanger sequencing, which is considered the clinical "gold standard"...
September 2016: Molecular Genetics & Genomic Medicine
Carmencita D Padilla, Eva Maria Cutiongco-de la Paz
Genetics and genomic medicine in the Philippines.
September 2016: Molecular Genetics & Genomic Medicine
Maximilian Muenke
Mentors without Borders is a proposed international mentoring network that allows trainee geneticists to identify mentors from a list of volunteers who are not at one's own institution. It is an experiment, a matchmaker between a junior and a senior professional. These mentors do not replace the mentors at the home institution but allow the mentee, if desired, to identify mentors outside of their own institution. We envision that different ways of communicating and/or different mentor-mentee relationships may prove beneficial to the trainee and the mentor...
September 2016: Molecular Genetics & Genomic Medicine
Tom Dubov, Hagit Toledano-Alhadef, Felix Bokstein, Shlomi Constantini, Shay Ben-Shachar
BACKGROUND: Neurofibromatosis type 1 (NF1) is the most common autosomal dominant neurocutaneous disease with a prevalence of 1:2500. Approximately, 50% of the cases are sporadic. Advanced paternal age is associated with germline mutations and autosomal diseases. We aimed to use NF1 as a paradigm to study the effect of parental age on sporadic mutation rates for both advanced and younger parental ages. METHODS: The medical charts of 118 NF1 pediatric patients followed in a specialized Israeli NF1 clinic were evaluated...
July 2016: Molecular Genetics & Genomic Medicine
Shahinaz M Gadalla, Payal P Khincha, Hormuzd A Katki, Neelam Giri, Jason Y Y Wong, Stephen Spellman, Jack A Yanovski, Joan C Han, Immaculata De Vivo, Blanche P Alter, Sharon A Savage
BACKGROUND: Telomere length <1st percentile-for-age in leukocyte subsets by flow cytometry with fluorescence in situ hybridization (flow FISH) is highly sensitive and specific in diagnosing patients with dyskeratosis congenita (DC), a telomere biology disorder. METHODS: We evaluated the clinical utility of the high-throughput quantitative real-time PCR (qPCR) relative telomere length (RTL) measurement as a diagnostic test for DC in patients with a priori clinical and/or genetic DC diagnoses...
July 2016: Molecular Genetics & Genomic Medicine
Rhalena A Thomas, Amirthagowri Ambalavanan, Guy A Rouleau, Philip A Barker
BACKGROUND: The protein NgR1 is encoded by RTN4R, a gene linked to schizophrenia. We previously reported NgR1 as receptor for the epilepsy-linked protein LGI1. NgR1 regulates synapse number and synaptic plasticity, whereas LGI1 antagonizes NgR1 signaling and promotes synapse formation. Impairments in synapse formation are common in neurological disease and we hypothesized that an LGI1-NgR1 signaling pathway may contribute to the development of schizophrenia. METHODS: We screened two unrelated schizophrenic populations for variants in RTN4R and LGI1 using whole exome sequencing and Sanger sequencing...
July 2016: Molecular Genetics & Genomic Medicine
Eva König, Johannes Rainer, Francisco S Domingues
BACKGROUND: Although several methods have been proposed for predicting the effects of genetic variants and their role in disease, it is still a challenge to identify and prioritize pathogenic variants within sequencing studies. METHODS: Here, we compare different variant and gene-specific features as well as existing methods and investigate their best combination to explore potential performance gains. RESULTS: We found that combining the number of "biological process" Gene Ontology annotations of a gene with the methods PON-P2, and PROVEAN significantly improves prediction of pathogenic variants, outperforming all individual methods...
July 2016: Molecular Genetics & Genomic Medicine
Jeppe D Andersen, Carlotta Pietroni, Peter Johansen, Mikkel M Andersen, Vania Pereira, Claus Børsting, Niels Morling
BACKGROUND: The color of the eyes is one of the most prominent phenotypes in humans and it is often used to describe the appearance of an individual. The intensity of pigmentation in the iris is strongly associated with one single-nucleotide polymorphism (SNP), rs12913832:A>G that is located in the promotor region of OCA2 (OMIM #611409). Nevertheless, many eye colors cannot be explained by only considering rs12913832:A>G. METHODS: In this study, we searched for additional variants in OCA2 to explain human eye color by sequencing a 500 kbp region, encompassing OCA2 and its promotor region...
July 2016: Molecular Genetics & Genomic Medicine
Xiangqing Sun, Robert Elston, Gary W Falk, William M Grady, Ashley Faulx, Sumeet K Mittal, Marcia I Canto, Nicholas J Shaheen, Jean S Wang, Prasad G Iyer, Julian A Abrams, Joseph E Willis, Kishore Guda, Sanford Markowitz, Jill S Barnholtz-Sloan, Apoorva Chandar, Wendy Brock, Amitabh Chak
BACKGROUND: Familial aggregation and segregation analysis studies have provided evidence of a genetic basis for esophageal adenocarcinoma (EAC) and its premalignant precursor, Barrett's esophagus (BE). We aim to demonstrate the utility of linkage analysis to identify the genomic regions that might contain the genetic variants that predispose individuals to this complex trait (BE and EAC). METHODS: We genotyped 144 individuals in 42 multiplex pedigrees chosen from 1000 singly ascertained BE/EAC pedigrees, and performed both model-based and model-free linkage analyses, using S...
July 2016: Molecular Genetics & Genomic Medicine
Stephanie S Yee, David B Lieberman, Tatiana Blanchard, JulieAnn Rader, Jianhua Zhao, Andrea B Troxel, Daniel DeSloover, Alan J Fox, Robert D Daber, Bijal Kakrecha, Shrey Sukhadia, George K Belka, Angela M DeMichele, Lewis A Chodosh, Jennifer J D Morrissette, Erica L Carpenter
BACKGROUND: Next-generation sequencing (NGS) of surgically resected solid tumor samples has become integral to personalized medicine approaches for cancer treatment and monitoring. Liquid biopsies, or the enrichment and characterization of circulating tumor cells (CTCs) from blood, can provide noninvasive detection of evolving tumor mutations to improve cancer patient care. However, the application of solid tumor NGS approaches to circulating tumor samples has been hampered by the low-input DNA available from rare CTCs...
July 2016: Molecular Genetics & Genomic Medicine
Benjamin D Solomon, Teresa Lee, Anh-Dao Nguyen, Tyra G Wolfsberg
No abstract text is available yet for this article.
July 2016: Molecular Genetics & Genomic Medicine
Teresa Pàmpols, Feliciano J Ramos, Pablo Lapunzina, Ignasi Gozalo-Salellas, Luis A Pérez-Jurado, Aurora Pujol
A view on clinical genetics and genomics in Spain: of challenges and opportunities.
July 2016: Molecular Genetics & Genomic Medicine
Nara L Sobreira, David Valle
No abstract text is available yet for this article.
July 2016: Molecular Genetics & Genomic Medicine
Tania Djémié, Sarah Weckhuysen, Sarah von Spiczak, Gemma L Carvill, Johanna Jaehn, Anna-Kaisa Anttonen, Eva Brilstra, Hande S Caglayan, Carolien G de Kovel, Christel Depienne, Eija Gaily, Elena Gennaro, Beatriz G Giraldez, Padhraig Gormley, Rosa Guerrero-López, Renzo Guerrini, Eija Hämäläinen, Corinna Hartmann, Laura Hernandez-Hernandez, Helle Hjalgrim, Bobby P C Koeleman, Eric Leguern, Anna-Elina Lehesjoki, Johannes R Lemke, Costin Leu, Carla Marini, Jacinta M McMahon, Davide Mei, Rikke S Møller, Hiltrud Muhle, Candace T Myers, Caroline Nava, Jose M Serratosa, Sanjay M Sisodiya, Ulrich Stephani, Pasquale Striano, Marjan J A van Kempen, Nienke E Verbeek, Sunay Usluer, Federico Zara, Aarno Palotie, Heather C Mefford, Ingrid E Scheffer, Peter De Jonghe, Ingo Helbig, Arvid Suls
BACKGROUND: Sanger sequencing, still the standard technique for genetic testing in most diagnostic laboratories and until recently widely used in research, is gradually being complemented by next-generation sequencing (NGS). No single mutation detection technique is however perfect in identifying all mutations. Therefore, we wondered to what extent inconsistencies between Sanger sequencing and NGS affect the molecular diagnosis of patients. Since mutations in SCN1A, the major gene implicated in epilepsy, are found in the majority of Dravet syndrome (DS) patients, we focused on missed SCN1A mutations...
July 2016: Molecular Genetics & Genomic Medicine
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