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Exome sequencing

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https://www.readbyqxmd.com/read/28821934/whole-exome-sequencing-to-identify-the-cause-of-congenital-sensorineural-hearing-loss-in-carriers-of-a-heterozygous-gjb2-mutation
#1
Thomas Parzefall, Alexandra Frohne, Martin Koenighofer, Andreas Kirchnawy, Berthold Streubel, Christian Schoefer, Klemens Frei, Trevor Lucas
Bi-allelic variations in the gap junction protein beta-2 (GJB2) gene cause up to 50% of cases of newborn hearing loss. Heterozygous pathogenic GJB2 variations are also fivefold overrepresented in idiopathic patient groups compared to the normal-hearing population. Whether hearing loss in this group is due to unidentified additional variations within GJB2 or variations in other deafness genes is unknown in most cases. Whole-exome sequencing offers an effective approach in the search for causative variations in patients with Mendelian diseases...
August 18, 2017: European Archives of Oto-rhino-laryngology
https://www.readbyqxmd.com/read/28821231/novel-mutations-in-pank2-and-pla2g6-genes-in-patients-with-neurodegenerative-disorders-two-case-reports
#2
Hassan Dastsooz, Hamid Nemati, Mohammad Ali Farazi Fard, Majid Fardaei, Mohammad Ali Faghihi
BACKGROUND: Neurodegeneration with brain iron accumulation (NBIA) is a genetically heterogeneous group of disorders associated with progressive impairment of movement, vision, and cognition. The disease is initially diagnosed on the basis of changes in brain magnetic resonance imaging which indicate an abnormal brain iron accumulation in the basal ganglia. However, the diagnosis of specific types should be based on both clinical findings and molecular genetic testing for genes associated with different types of NBIA, including PANK2, PLA2G6, C19orf12, FA2H, ATP13A2, WDR45, COASY, FTL, CP, and DCAF17...
August 18, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28821228/sg-adviser-mtdna-a-web-server-for-mitochondrial-dna-annotation-with-data-from-200-samples-of-a-healthy-aging-cohort
#3
Manuel Rueda, Ali Torkamani
BACKGROUND: Whole genome and exome sequencing usually include reads containing mitochondrial DNA (mtDNA). Yet, state-of-the-art pipelines and services for human nuclear genome variant calling and annotation do not handle mitochondrial genome data appropriately. As a consequence, any researcher desiring to add mtDNA variant analysis to their investigations is forced to explore the literature for mtDNA pipelines, evaluate them, and implement their own instance of the desired tool. This task is far from trivial, and can be prohibitive for non-bioinformaticians...
August 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28820917/whole-exome-sequencing-of-lacrimal-gland-adenoid-cystic-carcinoma
#4
David W Sant, Wensi Tao, Matthew G Field, Daniel Pelaez, Ke Jin, Anthony Capobianco, Sander R Dubovy, David T Tse, Gaofeng Wang
Purpose: To identify genomic mutations in lacrimal gland adenoid cystic carcinoma (LGACC) samples from patients. Methods: Genomic DNA was extracted from LGACC specimens. Whole exome sequencing (exome-seq) was conducted to screen for mutations. Capillary sequencing was performed to verify mutations in genes shared by multiple samples. Luciferase assays were used to evaluate functional consequences of NOTCH1 mutations. Results: The mutation profile of LGACC was complicated...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28820624/retinopathy-and-optic-atrophy-expanding-the-phenotypic-spectrum-of-pathogenic-variants-in-the-aars2-gene
#5
Jason H Peragallo, Stephanie Keller, Marjo S van der Knaap, Bruno P Soares, Suma P Shankar
BACKGROUND: Optic atrophy may be the sequela of optic nerve injury due to any insult, including isolated and syndromic genetic diseases. Alanyl-tRNA synthetase 2 (AARS2) pathogenic variants have been reported to cause leukodystrophy with ovarian failure, and cardiomyopathy (#615889) as well as combined oxidative phosphorylation deficiency-8 (#614096). We report a young child who presented with decreased vision due to optic atrophy and was found to harbor missense variants in the AARS2 gene expanding the phenotypic expression of the AARS2 gene...
August 18, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28819847/negative-enrichment-and-isolation-of-circulating-tumor-cells-for-whole-genome-amplification
#6
Nisha Kanwar, Susan J Done
Circulating tumor cells (CTCs) are a rare population of cells found in the peripheral blood of patients with many types of cancer such as breast, prostate, colon, and lung cancers. Higher numbers of these cells in blood are associated with a poorer prognosis of patients. Genomic profiling of CTCs would help characterize markers specific for the identification of these cells in blood, and also define genomic alterations that give these cells a metastatic advantage over other cells in the primary tumor. Here, we describe an immunomagnetic method to enrich CTCs from the blood of patients with breast cancer, followed by single-cell laser capture microdissection to isolate single CTCs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28819774/whole-exome-sequencing-of-wild-derived-inbred-strains-of-mice-improves-power-to-link-phenotype-and-genotype
#7
Peter L Chang, Emily Kopania, Sara Keeble, Brice A J Sarver, Erica Larson, Annie Orth, Khalid Belkhir, Pierre Boursot, Fran├žois Bonhomme, Jeffrey M Good, Matthew D Dean
The house mouse is a powerful model to dissect the genetic basis of phenotypic variation, and serves as a model to study human diseases. Despite a wealth of discoveries, most classical laboratory strains have captured only a small fraction of genetic variation known to segregate in their wild progenitors, and existing strains are often related to each other in complex ways. Inbred strains of mice independently derived from natural populations have the potential to increase power in genetic studies with the addition of novel genetic variation...
August 17, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28819563/novel-clcn7-compound-heterozygous-mutations-in-intermediate-autosomal-recessive-osteopetrosis
#8
Nana Okamoto, Tomohiro Kohmoto, Takuya Naruto, Kiyoshi Masuda, Takahide Komori, Issei Imoto
Osteopetrosis is a heritable disorder of the skeleton that is characterized by increased bone density on radiographs caused by defects in osteoclast formation and function. Mutations in >10 genes are identified as causative for this clinically and genetically heterogeneous disease in humans. We report two novel missense variations in a compound heterozygous state in the CLCN7 gene, detected through targeted exome sequencing, in a 15-year-old Japanese female with intermediate autosomal recessive osteopetrosis...
2017: Human Genome Variation
https://www.readbyqxmd.com/read/28819016/a-syndromic-extreme-insulin-resistance-caused-by-biallelic-poc1a-mutations-in-exon-10
#9
Elisa Giorgio, Elisa Rubino, Alessandro Bruselles, Simone Pizzi, Innocenzo Rainero, Sergio Duca, Fabio Sirchia, Barbara Pasini, Marco Tartaglia, Alfredo Brusco
POC1A encodes a protein with a role in centriole assembly and stability, and in ciliogenesis. Biallelic loss of function mutations affecting POC1A cause SOFT syndrome, an ultra-rare condition characterized by short stature, onychodysplasia, facial dysmorphism and hypotrichosis. Using exome sequencing, we identified a homozygous frameshift mutation (c.1047_1048dupC; p.G337Rfs*25) in a patient presenting with short stature, facial hirsutism, alopecia, dyslipidemia and extreme insulin resistance. The truncating variant affected exon 10, which is retained in only two of the three POC1A mature RNAs, due to alternative processing of the transcript...
August 17, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28817240/prenatal-presentation-of-mabry-syndrome-with-congenital-diaphragmatic-hernia-and-phenotypic-overlap-with-fryns-syndrome
#10
Kara K Reynolds, Jane Juusola, Gregory M Rice, Philip F Giampietro
We report on a family in which initial features were compatible with Fryns syndrome. The first sibling was a stillborn female with a left diaphragmatic hernia (DH). Her clinical features overlapped with Fryns syndrome. The second pregnancy, a male fetus, was followed for polyhydramnios, hypoplastic mandible, mild enlargement of the fetal bladder, hydronephrosis, and rocker bottom foot deformities. He had facial features similar to his sibling and a large cleft of the secondary palate, small jaw, and secundum atrial septal defect...
August 17, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28817238/stakeholders-in-psychiatry-and-their-attitudes-toward-receiving-pertinent-and-incident-findings-in-genomic-research
#11
Anna Sundby, Merete W Boolsen, Kristoffer S Burgdorf, Henrik Ullum, Thomas F Hansen, Anna Middleton, Ole Mors
Increasingly more psychiatric research studies use whole genome sequencing or whole exome sequencing. Consequently, researchers face difficult questions, such as which genomic findings to return to research participants and how. This study aims to gain more knowledge on the attitudes among potential research participants and health professionals toward receiving pertinent and incidental findings. A cross-sectional online survey was developed to investigate the attitudes among research participants toward receiving genomic findings...
August 17, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28817112/monoallelic-and-biallelic-creb3l1-variant-causes-mild-and-severe-osteogenesis-imperfecta-respectively
#12
Rachel B Keller, Thao T Tran, Shawna M Pyott, Melanie G Pepin, Ravi Savarirayan, George McGillivray, Deborah A Nickerson, Michael J Bamshad, Peter H Byers
PurposeOsteogenesis imperfecta (OI) is a heritable skeletal dysplasia. Dominant pathogenic variants in COL1A1 and COL1A2 explain the majority of OI cases. At least 15 additional genes have been identified, but those still do not account for all OI phenotypes that present. We sought the genetic cause of mild and lethal OI phenotypes in an unsolved family.MethodsWe performed exome sequencing on seven members of the family, both affected and unaffected.ResultsWe identified a variant in cyclic AMP responsive element binding protein 3-like 1 (CREB3L1) in a consanguineous family...
August 17, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28817111/prospective-cohort-study-for-identification-of-underlying-genetic-causes-in-neonatal-encephalopathy-using-whole-exome-sequencing
#13
Theodora U J Bruun, Caro-Lyne DesRoches, Diane Wilson, Vann Chau, Tadashi Nakagawa, Masahiro Yamasaki, Shinya Hasegawa, Toshiyuki Fukao, Christian Marshall, Saadet Mercimek-Andrews
PurposeNeonatal encephalopathy, which is characterized by a decreased level of consciousness, occurs in 1-7/1,000 live-term births. In more than half of term newborns, there is no identifiable etiological factor. To identify underlying genetic defects, we applied whole-exome sequencing (WES) in term newborns with neonatal encephalopathy as a prospective cohort study.MethodsTerm newborns with neonatal encephalopathy and no history of perinatal asphyxia were included. WES was performed using patient and both parents' DNA...
August 17, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28816949/whole-exome-sequencing-identifies-a-kcnj12-mutation-as-a-cause-of-familial-dilated-cardiomyopathy
#14
Hai-Xin Yuan, Kai Yan, Dong-Yan Hou, Zhi-Yong Zhang, Hua Wang, Xin Wang, Juan Zhang, Xiao-Rong Xu, Yan-Hong Liang, Wen-Shu Zhao, Lin Xu, Lin Zhang
Dilated cardiomyopathy (DCM) is characterized by left ventricular dilation, and is associated with systolic dysfunction and increased action potential duration. Approximately 50% of DCM cases are caused by inherited gene mutations with genetic and phenotypic heterogeneity. Next generation sequencing may be useful in screening unknown mutations in such cases.A family was identified with DCM, in which the affected family members developed heart failure, arrhythmia, and sudden death. Probands and 4 affected family members underwent whole exome sequencing (WES), bioinformatics methods, and gene annotation to identify potentially causative variants...
August 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28816351/recent-advances-in-genomic-profiling-of-adenosquamous-carcinoma-of-the-pancreas
#15
Rebecca Marcus, Anirban Maitra, Jason Roszik
Adenosquamous carcinoma of the pancreas (ASCP) is a mixed tumor type which contains squamous cell carcinoma and also ductal adenocarcinoma components. Due to the rarity of this malignancy, only very limited genomic profiling has been performed. A recent paper by Fang et al. published in The Journal of Pathology contributed to our knowledge of genomic alterations by performing whole genome and exome sequencing of 17 ASCP tumors. They found major genomic similarities to pancreatic ductal adenocarcinoma; however, the p53 pathway was altered in a greater proportion of cases, while a high frequency of 3p loss was a distinct copy number alteration pattern observed in ASCP...
August 17, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28815955/the-role-of-iqsec2-in-syndromic-intellectual-disability-narrowing-the-diagnostic-odyssey
#16
Benjamin M Helm, Zoe Powis, Carlos E Prada, Olga L Casasbuenas-Alarcon, Tonya Balmakund, G B Schaefer, Stephen G Kahler, Julie Kaylor, Susan Winter, Yuri A Zarate, Samantha A Schrier Vergano
While X-linked intellectual disability (XLID) syndromes pose a diagnostic challenge for clinicians, an increasing number of recognized disorders and their genetic etiologies are providing answers for patients and their families. The availability of clinical exome sequencing is broadening the ability to identify mutations in genes previously unrecognized as causing XLID. In recent years, the IQSEC2 gene, located at Xp11.22, has emerged as the cause of multiple cases of both nonsyndromic and syndromic XLID. Herein we present a case series of six individuals (five males, one female) with intellectual disability and seizures found to have alterations in IQSEC2...
August 17, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28815944/neonatal-fractures-as-a-presenting-feature-of-lmod3-associated-congenital-myopathy
#17
Megan Abbott, Mahim Jain, Rachel Pferdehirt, Yuqing Chen, Alyssa Tran, Mehmet B Duz, Mehmet Seven, Richard A Gibbs, Donna Muzny, Brendan Lee, Ronit Marom, Lindsay C Burrage
Nemaline myopathy is a rare inherited disorder characterized by weakness, hypotonia, and depressed deep tendon reflexes. It is clinically and genetically heterogeneous, with the most severe phenotype presenting as perinatal akinesia, severe muscle weakness, feeding difficulties and respiratory failure, leading to early mortality. Pathogenic variants in 12 genes, encoding components of the sarcomere or factors related to myogenesis, have been reported in patients affected with the disorder. Here, we describe an early, lethal presentation of decreased fetal movements, hypotonia, muscle weakness, and neonatal respiratory failure requiring ventilator support in three siblings from a consanguineous family...
August 16, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28815929/aggregation-of-population-based-genetic-variation-over-protein-domain-homologues-and-its-potential-use-in-genetic-diagnostics
#18
Laurens Wiel, Hanka Venselaar, Joris A Veltman, Gerrit Vriend, Christian Gilissen
Whole exomes of patients with a genetic disorder are nowadays routinely sequenced but interpretation of the identified genetic variants remains a major challenge. The increased availability of population-based human genetic variation has given rise to measures of genetic tolerance that have been used, for example, to predict disease-causing genes in neurodevelopmental disorders. Here, we investigated whether combining variant information from homologous protein domains can improve variant interpretation. For this purpose, we developed a framework that maps population variation and known pathogenic mutations onto 2,750 "meta-domains"...
August 16, 2017: Human Mutation
https://www.readbyqxmd.com/read/28815891/cystic-kidneys-in-fetal-walker-warburg-syndrome-with-pomt2-mutation-intrafamilial-phenotypic-variability-in-four-siblings-and-review-of-literature
#19
Marwa M Nabhan, Nour ElKhateeb, Daniela A Braun, Sungho Eun, Sahar N Saleem, Heon YungGee, Friedhelm Hildebrandt, Neveen A Soliman
Walker-Warburg syndrome (WWS) is a severe form of congenital muscular dystrophy secondary to ╬▒-dystroglycanopathy with muscle, brain, and eye abnormalities often leading to death in the first weeks of life. It is transmitted in an autosomal recessive pattern, and has been linked to at least 15 different genes; including protein O-mannosyltransferase 1 (POMT1), protein O-mannosyltransferase 2 (POMT2), protein O-mannose beta-1,2-N acetylglucosaminyltransferase (POMGNT1), fukutin (FKTN), isoprenoid synthase domain-containing protein (ISPD), and other genes...
August 17, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28815871/clinical-and-molecular-characterization-of-de-novo-loss-of-function-variants-in-hnrnpu
#20
Magalie S Leduc, Hsiao-Tuan Chao, Chunjing Qu, Magdalena Walkiewicz, Rui Xiao, Pilar Magoulas, Shujuan Pan, Joke Beuten, Weimin He, Jonathan A Bernstein, Christian P Schaaf, Fernando Scaglia, Christine M Eng, Yaping Yang
DNA alterations in the 1q43-q44 region are associated with syndromic neurodevelopmental disorders characterized by global developmental delay, intellectual disability, dysmorphic features, microcephaly, seizures, and agenesis of the corpus callosum. HNRNPU is located within the 1q43-q44 region and mutations in the gene have been reported in patients with early infantile epileptic encephalopathy. Here, we report on the clinical presentation of four patients with de novo heterozygous HNRNPU loss-of-function mutations detected by clinical whole exome sequencing: c...
August 16, 2017: American Journal of Medical Genetics. Part A
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