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https://www.readbyqxmd.com/read/28433079/utilization-of-whole-exome-next-generation-sequencing-variant-read-frequency-for-detection-of-lesion-specific-somatic-loss-of-heterozygosity-in-a-neurofibromatosis-type-1-cohort-with-tibial-pseudarthrosis
#1
Rebecca L Margraf, Chad VanSant-Webb, David Sant, John Carey, Heather Hanson, Jacques D'Astous, Dave Viskochil, David A Stevenson, Rong Mao
A subset of neurofibromatosis type 1 patients develop tibial dysplasia, which can lead to pseudarthrosis. The tissue from the tibial pseudarthrosis region commonly has a somatic second hit in NF1: single-nucleotide variants, small deletions, or loss of heterozygosity (LOH). We used exome next-generation sequencing (NGS) variant frequency data (allelic imbalance analysis) to detect somatic LOH in pseudarthrosis tissue from three individuals with clinically and diagnostically confirmed neurofibromatosis type 1, and verified the results with microarray...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28432085/acute-myeloid-leukaemia-in-a-case-with-tatton-brown-rahman-syndrome-the-peculiar-dnmt3a-r882-mutation
#2
Iris H I M Hollink, Ans M W van den Ouweland, H Berna Beverloo, Susan T C J M Arentsen-Peters, C Michel Zwaan, Anja Wagner
BACKGROUND: Recently a novel syndromic form of overgrowth with intellectual disability and distinct facial features was identified caused by constitutional mutations in the epigenetic regulator DNA-methyltransferase 3A (DNMT3A), referred to as Tatton-Brown-Rahman syndrome (TBRS). Somatically acquired mutations in DNMT3A occur in haematological malignancies and are frequently present in acute myeloid leukaemia (AML) affecting in more than 50% the arginine residue at position 882 (R882)...
April 21, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28432012/novel-compound-heterozygous-mutations-in-the-pex1-gene-in-two-chinese-newborns-with-zellweger-syndrome-based-on-whole-exome-sequencing
#3
Meng-Meng Ge, LiYuan Hu, ZhiHua Li, GuoQiang Cheng, Kai Yan, YanTing Kong, HuiJun Wang, Lin Yang, WenHao Zhou
Peroxisome biogenesis disorders (PBDs) represent a spectrum of human genetic disorders that are characterized by damaged peroxisome assembly. In the newborn period, the characteristics of affected patients include dysmorphic facial features, neonatal hypotonia, seizures, ocular abnormalities, poor feeding, liver cysts with hepatic dysfunction and skeletal defects. These can be caused by a defect in at least 14 different PEX genes. In this study, whole-exome sequencing (WES) was performed on samples from two Chinese newborns with clinical features of Zellweger syndrome...
April 18, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28431867/whole-exome-sequencing-identification-of-novel-candidate-genes-in-patients-with-proliferative-diabetic-retinopathy
#4
Cindy Ung, Angie V Sanchez, Lishuang Shen, Samaneh Davoudi, Tina Ahmadi, Daniel Navarro-Gomez, Ching J Chen, Heather Hancock, Alan Penman, Suzanne Hoadley, Mark Consugar, Carlos Restrepo, Vinay A Shah, Joseph F Arboleda-Velasquez, Lucia Sobrin, Xiaowu Gai, Leo A Kim
Rare or novel gene variants in patients with proliferative diabetic retinopathy may contribute to disease development. We performed whole exome sequencing (WES) on patients at the phenotypic extremes of diabetic retinal complications: 57 patients diagnosed with proliferativediabetic retinopathy (PDR) as cases and 13 patients with no diabetic retinopathy despite at least 10 years of type 2 diabetes as controls. Thirty-one out of the 57 cases and all 13 controls were from the African American Proliferative Diabetic Retinopathy Study (AA)...
April 18, 2017: Vision Research
https://www.readbyqxmd.com/read/28431612/xeroderma-pigmentosum-complementation-group-f-a-rare-cause-of-cerebellar-ataxia-with-chorea
#5
G Carré, C Marelli, M Anheim, C Geny, M Renaud, H R Rezvani, M Koenig, C Guissart, C Tranchant
The complementation group F of Xeroderma pigmentosum (XP-F) is rare in the Caucasian population, and usually devoid of neurological symptoms. We report two cases, both Caucasian, who exhibited progressive cerebellar ataxia, chorea, a mild subcortical frontal cognitive impairment, and in one case severe polyneuropathy. Brain MRI demonstrated cerebellar (2/2) and cortical (1/2) atrophy. Both patients had only mild sunburn sensitivity and no skin cancer. Mini-exome sequencing approach revealed in ERCC4, two heterozygous mutations, one of which was never described (c...
May 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28429804/identifying-tagging-snps-for-african-specific-genetic-variation-from-the-african-diaspora-genome
#6
Henry Richard Johnston, Yi-Juan Hu, Jingjing Gao, Timothy D O'Connor, Gonçalo R Abecasis, Genevieve L Wojcik, Christopher R Gignoux, Pierre-Antoine Gourraud, Antoine Lizee, Mark Hansen, Rob Genuario, Dave Bullis, Cindy Lawley, Eimear E Kenny, Carlos Bustamante, Terri H Beaty, Rasika A Mathias, Kathleen C Barnes, Zhaohui S Qin
A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429735/phylogenetic-analysis-of-metastatic-progression-in-breast-cancer-using-somatic-mutations-and-copy-number-aberrations
#7
David Brown, Dominiek Smeets, Borbála Székely, Denis Larsimont, A Marcell Szász, Pierre-Yves Adnet, Françoise Rothé, Ghizlane Rouas, Zsófia I Nagy, Zsófia Faragó, Anna-Mária Tőkés, Magdolna Dank, Gyöngyvér Szentmártoni, Nóra Udvarhelyi, Gabriele Zoppoli, Lajos Pusztai, Martine Piccart, Janina Kulka, Diether Lambrechts, Christos Sotiriou, Christine Desmedt
Several studies using genome-wide molecular techniques have reported various degrees of genetic heterogeneity between primary tumours and their distant metastases. However, it has been difficult to discern patterns of dissemination owing to the limited number of patients and available metastases. Here, we use phylogenetic techniques on data generated using whole-exome sequencing and copy number profiling of primary and multiple-matched metastatic tumours from ten autopsied patients to infer the evolutionary history of breast cancer progression...
April 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28429724/clonal-evolution-in-myelodysplastic-syndromes
#8
Pedro da Silva-Coelho, Leonie I Kroeze, Kenichi Yoshida, Theresia N Koorenhof-Scheele, Ruth Knops, Louis T van de Locht, Aniek O de Graaf, Marion Massop, Sarah Sandmann, Martin Dugas, Marian J Stevens-Kroef, Jaroslav Cermak, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Theo de Witte, Nicole M A Blijlevens, Petra Muus, Gerwin Huls, Bert A van der Reijden, Seishi Ogawa, Joop H Jansen
Cancer development is a dynamic process during which the successive accumulation of mutations results in cells with increasingly malignant characteristics. Here, we show the clonal evolution pattern in myelodysplastic syndrome (MDS) patients receiving supportive care, with or without lenalidomide (follow-up 2.5-11 years). Whole-exome and targeted deep sequencing at multiple time points during the disease course reveals that both linear and branched evolutionary patterns occur with and without disease-modifying treatment...
April 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28428906/tbc1d24-mutations-in-a-sibship-with-multifocal-polymyoclonus
#9
Adeline Ngoh, Jose Bras, Rita Guerreiro, Amy McTague, Joanne Ng, Esther Meyer, W Kling Chong, Stewart Boyd, Linda MacLellan, Martin Kirkpatrick, Manju A Kurian
BACKGROUND: Advances in molecular genetic technologies have improved our understanding of genetic causes of rare neurological disorders with features of myoclonus. CASE REPORT: A family with two affected siblings, presenting with multifocal polymyoclonus and neurodevelopmental delay, was recruited for whole-exome sequencing following unyielding diagnostic neurometabolic investigations. Compound heterozygous mutations in TBC1D24, a gene previously associated with various epilepsy phenotypes and hearing loss, were identified in both siblings...
2017: Tremor and Other Hyperkinetic Movements
https://www.readbyqxmd.com/read/28427458/whole-exome-sequencing-identifies-novel-candidate-predisposition-genes-for-familial-polycythemia-vera
#10
Elina A M Hirvonen, Esa Pitkänen, Kari Hemminki, Lauri A Aaltonen, Outi Kilpivaara
BACKGROUND: Polycythemia vera (PV), characterized by massive production of erythrocytes, is one of the myeloproliferative neoplasms. Most patients carry a somatic gain-of-function mutation in JAK2, c.1849G > T (p.Val617Phe), leading to constitutive activation of JAK-STAT signaling pathway. Familial clustering is also observed occasionally, but high-penetrance predisposition genes to PV have remained unidentified. RESULTS: We studied the predisposition to PV by exome sequencing (three cases) in a Finnish PV family with four patients...
April 20, 2017: Human Genomics
https://www.readbyqxmd.com/read/28427446/respiratory-chain-complex-iii-deficiency-due-to-mutated-bcs1l-a-novel-phenotype-with-encephalomyopathy-partially-phenocopied-in-a-bcs1l-mutant-mouse-model
#11
Saara Tegelberg, Nikica Tomašić, Jukka Kallijärvi, Janne Purhonen, Eskil Elmér, Eva Lindberg, David Gisselsson Nord, Maria Soller, Nicole Lesko, Anna Wedell, Helene Bruhn, Christoph Freyer, Henrik Stranneheim, Rolf Wibom, Inger Nennesmo, Anna Wredenberg, Erik A Eklund, Vineta Fellman
BACKGROUND: Mitochondrial diseases due to defective respiratory chain complex III (CIII) are relatively uncommon. The assembly of the eleven-subunit CIII is completed by the insertion of the Rieske iron-sulfur protein, a process for which BCS1L protein is indispensable. Mutations in the BCS1L gene constitute the most common diagnosed cause of CIII deficiency, and the phenotypic spectrum arising from mutations in this gene is wide. RESULTS: A case of CIII deficiency was investigated in depth to assess respiratory chain function and assembly, and brain, skeletal muscle and liver histology...
April 20, 2017: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/28427232/embryonic-signature-distinguishes-pediatric-and-adult-rhabdoid-tumors-from-other-smarcb1-deficient-cancers
#12
Wilfrid Richer, Julien Masliah-Planchon, Nathalie Clement, Irene Jimenez, Laetitia Maillot, David Gentien, Benoît Albaud, Walid Chemlali, Christine Galant, Frederique Larousserie, Pascaline Boudou-Rouquette, Amaury Leruste, Celine Chauvin, Zhi Yan Han, Jean-Michel Coindre, Pascale Varlet, Paul Freneaux, Dominique Ranchère-Vince, Olivier Delattre, Franck Bourdeaut
Extra-cranial rhabdoid tumors (RT) are highly aggressive malignancies of infancy, characterized by undifferentiated histological features and loss of SMARCB1 expression. The diagnosis is all the more challenging that other poorly differentiated cancers lose SMARCB1 expression, such as epithelioid sarcomas (ES), renal medullary carcinomas (RMC) or undifferentiated chordomas (UC). Moreover, late cases occurring in adults are now increasingly reported, raising the question of differential diagnoses and emphasizing nosological issues...
March 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28427202/clinical-implications-of-genomic-profiles-in-metastatic-breast-cancer-with-a-focus-on-tp53-and-pik3ca-the-most-frequently-mutated-genes
#13
Ji-Yeon Kim, Eunjin Lee, Kyunghee Park, Woong-Yang Park, Hae Hyun Jung, Jin Seok Ahn, Young-Hyuck Im, Yeon Hee Park
Breast cancer (BC) has been genetically profiled through large-scale genome analyses. However, the role and clinical implications of genetic alterations in metastatic BC (MBC) have not been evaluated. Therefore, we conducted whole-exome sequencing (WES) and RNA-Seq of 37 MBC samples and targeted deep sequencing of another 29 MBCs. We evaluated somatic mutations from WES and targeted sequencing and assessed gene expression and performed pathway analysis from RNA-Seq. In this analysis, PIK3CA was the most commonly mutated gene in estrogen receptor (ER)-positive BC, while in ER-negative BC, TP53 was the most commonly mutated gene (p = 0...
March 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28426742/multiple-components-of-pka-and-tgf-%C3%AE-pathways-are-mutated-in-pseudomyxoma-peritonei
#14
Lilli Saarinen, Pirjo Nummela, Alexandra Thiel, Rainer Lehtonen, Petrus Järvinen, Heikki Järvinen, Lauri A Aaltonen, Anna Lepistö, Sampsa Hautaniemi, Ari Ristimäki
Pseudomyxoma peritonei (PMP) is a subtype of mucinous adenocarcinoma mainly restricted to the peritoneal cavity and most commonly originating from the appendix. The genetic background of PMP is poorly understood and no targeted treatments are currently available for this fatal disease. While RAS signaling pathway is affected in most if not all PMP cases and over half of them also have a mutation in the GNAS gene, other genetic alterations and affected pathways are, to a large degree, poorly known. In this study, we sequenced whole coding genome of nine PMP tumors and paired normal tissues in order to identify additional, commonly mutated genes and signaling pathways affected in PMP...
2017: PloS One
https://www.readbyqxmd.com/read/28426234/the-otogl-p-arg925-variant-is-associated-with-moderate-hearing-loss-in-a-syrian-nonconsanguineous-family
#15
Rana Barake, Samer Abou-Rizk, Georges Nemer, Marc Bassim
AIMS: To screen for the genetic basis of congenital hearing loss in a Syrian family. METHODS: A Syrian patient living in Lebanon presented with moderate congenital hearing loss. The patient's large nonconsanguineous family was recruited. DNA was extracted from blood samples and sent for whole-exome sequencing. A detailed clinical examination along with audiograms was obtained for all subjects. RESULTS: Hearing loss was noted to be mild to moderate in the low and mid frequencies, sloping to moderate to severe in the high frequencies for all affected members...
April 20, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28425981/whole-exome-sequencing-on-deceased-fetuses-with-ultrasound-anomalies-expanding-our-knowledge-of-genetic-disease-during-fetal-development
#16
Carin L Yates, Kristin G Monaghan, Deborah Copenheaver, Kyle Retterer, Julie Scuffins, Cathlin R Kucera, Bethany Friedman, Gabriele Richard, Jane Juusola
PurposeThe aim of this study was to determine the diagnostic yield of whole-exome sequencing (WES) in fetuses with ultrasound anomalies that resulted in fetal demise or pregnancy termination. The results were also utilized to aid in the identification of candidate genes for fetal development and to expand the clinical phenotype of known genetic conditions.MethodsWES was performed on specimens from 84 deceased fetuses. Data were analyzed and final results were classified into one of four categories: positive, possible, negative, and candidate gene only...
April 20, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28425186/association-studies-of-low-frequency-coding-variants-in-nonsyndromic-cleft-lip-with-or-without-cleft-palate
#17
Elizabeth J Leslie, Jenna C Carlson, John R Shaffer, Carmen J Buxó, Eduardo E Castilla, Kaare Christensen, Frederic W B Deleyiannis, Leigh L Field, Jacqueline T Hecht, Lina Moreno, Ieda M Orioli, Carmencita Padilla, Alexandre R Vieira, George L Wehby, Eleanor Feingold, Seth M Weinberg, Jeffrey C Murray, Mary L Marazita
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a group of common human birth defects with complex etiology. Although genome-wide association studies have successfully identified a number of risk loci, these loci only account for about 20% of the heritability of orofacial clefts. The "missing" heritability may be found in rare variants, copy number variants, or interactions. In this study, we investigated the role of low-frequency variants genotyped in 1995 cases and 1626 controls on the Illumina HumanCore + Exome chip...
April 19, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28425089/high-diagnostic-yield-of-clinically-unidentifiable-syndromic-growth-disorders-by-targeted-exome-sequencing
#18
Yoo-Mi Kim, Yun-Jin Lee, Jae Hong Park, Hyoung-Doo Lee, Chong Kun Cheon, Su-Young Kim, Jae-Yeon Hwang, Ja-Hyun Jang, Han-Wook Yoo
As syndromic short stature and overgrowth are heterogeneous and the list of causative genes is rapidly expanding, there is an unmet need for identifying genetic causes based on conventional gene testing or karyotyping. Early diagnosis leads to the proper management of the patient and providing genetic counseling for family members at risk in a timely manner. We conducted targeted exome sequencing to identify the genetic causes of undiagnosed syndromic short stature or overgrowth in 15 pediatric patients from 13 families in Korea...
April 20, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28424332/improving-genetic-diagnosis-in-mendelian-disease-with-transcriptome-sequencing
#19
Beryl B Cummings, Jamie L Marshall, Taru Tukiainen, Monkol Lek, Sandra Donkervoort, A Reghan Foley, Veronique Bolduc, Leigh B Waddell, Sarah A Sandaradura, Gina L O'Grady, Elicia Estrella, Hemakumar M Reddy, Fengmei Zhao, Ben Weisburd, Konrad J Karczewski, Anne H O'Donnell-Luria, Daniel Birnbaum, Anna Sarkozy, Ying Hu, Hernan Gonorazky, Kristl Claeys, Himanshu Joshi, Adam Bournazos, Emily C Oates, Roula Ghaoui, Mark R Davis, Nigel G Laing, Ana Topf, Peter B Kang, Alan H Beggs, Kathryn N North, Volker Straub, James J Dowling, Francesco Muntoni, Nigel F Clarke, Sandra T Cooper, Carsten G Bönnemann, Daniel G MacArthur
Exome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25 to 50%. We explore the utility of transcriptome sequencing [RNA sequencing (RNA-seq)] as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare muscle disorders. We describe an integrated approach to analyze patient muscle RNA-seq, leveraging an analysis framework focused on the detection of transcript-level changes that are unique to the patient compared to more than 180 control skeletal muscle samples...
April 19, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28424246/enteropathy-associated-t-cell-lymphoma-subtypes-are-characterized-by-loss-of-function-of-setd2
#20
Andrea B Moffitt, Sarah L Ondrejka, Matthew McKinney, Rachel E Rempel, John R Goodlad, Chun Huat Teh, Sirpa Leppa, Susanna Mannisto, Panu E Kovanen, Eric Tse, Rex K H Au-Yeung, Yok-Lam Kwong, Gopesh Srivastava, Javeed Iqbal, Jiayu Yu, Kikkeri Naresh, Diego Villa, Randy D Gascoyne, Jonathan Said, Magdalena B Czader, Amy Chadburn, Kristy L Richards, Deepthi Rajagopalan, Nicholas S Davis, Eileen C Smith, Brooke C Palus, Tiffany J Tzeng, Jane A Healy, Patricia L Lugar, Jyotishka Datta, Cassandra Love, Shawn Levy, David B Dunson, Yuan Zhuang, Eric D Hsi, Sandeep S Dave
Enteropathy-associated T cell lymphoma (EATL) is a lethal, and the most common, neoplastic complication of celiac disease. Here, we defined the genetic landscape of EATL through whole-exome sequencing of 69 EATL tumors. SETD2 was the most frequently silenced gene in EATL (32% of cases). The JAK-STAT pathway was the most frequently mutated pathway, with frequent mutations in STAT5B as well as JAK1, JAK3, STAT3, and SOCS1 We also identified mutations in KRAS, TP53, and TERT Type I EATL and type II EATL (monomorphic epitheliotropic intestinal T cell lymphoma) had highly overlapping genetic alterations indicating shared mechanisms underlying their pathogenesis...
April 19, 2017: Journal of Experimental Medicine
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