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https://www.readbyqxmd.com/read/28190455/who-s-who-detecting-and-resolving-sample-anomalies-in-human-dna-sequencing-studies-with-peddy
#1
Brent S Pedersen, Aaron R Quinlan
The potential for genetic discovery in human DNA sequencing studies is greatly diminished if DNA samples from a cohort are mislabeled, swapped, or contaminated or if they include unintended individuals. Unfortunately, the potential for such errors is significant since DNA samples are often manipulated by several protocols, labs, or scientists in the process of sequencing. We have developed a software package, peddy, to identify and facilitate the remediation of such errors via interactive visualizations and reports comparing the stated sex, relatedness, and ancestry to what is inferred from the individual genotypes derived from whole-genome (WGS) or whole-exome (WES) sequencing...
January 30, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28186598/-a-boy-with-meier-gorlin-syndrome-carrying-a-novel-orc6-mutation-and-uniparental-disomy-of-chromosome-16
#2
Juan Li, Yu Ding, Guoying Chang, Qing Cheng, Xin Li, Jian Wang, Xiumin Wang, Yiping Shen
OBJECTIVE: To identify the genetic cause for a 11-year-old Chinese boy with Meier-Gorlin syndrome (MGS). METHODS: Chromosomal microarray analysis (CMA) was used to detect potential variations, while whole exome sequencing (WES) was used to identify sequence variants. Sanger sequencing was used to confirm the suspected variants. RESULTS: The boy has featured short stature, microtia, small patella, slender body build, craniofacial anomalies, and small testes with normal gonadotropin...
February 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28182608/prevalence-and-clinical-attributes-of-congenital-microcephaly-new-york-2013-2015
#3
Krishika A Graham, Deborah J Fox, Achala Talati, Cristian Pantea, Laura Brady, Sondra L Carter, Eric Friedenberg, Neil M Vora, Marilyn L Browne, Christopher T Lee
Congenital Zika virus infection can cause microcephaly and other severe fetal neurological anomalies (1). To inform microcephaly surveillance efforts and assess ascertainment sources, the New York State Department of Health and the New York City Department of Health and Mental Hygiene sought to determine the prevalence of microcephaly in New York during 2013-2015, before known importation of Zika virus infections. Suspected newborn microcephaly diagnoses were identified from 1) reports submitted by birth hospitals in response to a request and 2) queries of a hospital administrative discharge database for newborn microcephaly diagnoses...
February 10, 2017: MMWR. Morbidity and Mortality Weekly Report
https://www.readbyqxmd.com/read/28180026/chromosomal-microarrays-understanding-genetics-of-neurodevelopmental-disorders-and-congenital-anomalies
#4
REVIEW
Jill A Rosenfeld, Ankita Patel
Chromosomal microarray (CMA) testing, used to identify DNA copy number variations (CNVs), has helped advance knowledge about genetics of human neurodevelopmental disease and congenital anomalies. It has aided in discovering new CNV syndromes and uncovering disease genes. It has discovered CNVs that are not fully penetrant and/or cause a spectrum of phenotypes, including intellectual disability, autism, schizophrenia, and dysmorphisms. Such CNVs can pose challenges to genetic counseling. They also have helped increase knowledge of genetic risk factors for neurodevelopmental disease and raised awareness of possible shared etiologies among these variable phenotypes...
March 2017: Journal of Pediatric Genetics
https://www.readbyqxmd.com/read/28179367/genomic-rearrangements-in-arabidopsis-considered-as-quantitative-traits
#5
Martha Imprialou, André Kahles, Joshua G Steffen, Edward J Osborne, Xiangchao Gan, Janne Lempe, Amarjit Bhomra, Eric Belfield, Anne Visscher, Robert Greenhalgh, Nicholas P Harberd, Richard Goram, Jotun Hein, Alexandre Robert-Seilaniantz, Jonathan Jones, Oliver Stegle, Paula Kover, Miltos Tsiantis, Magnus Nordborg, Gunnar Rätsch, Richard M Clark, Richard Mott
To understand the population genetics of structural variants and their effects on phenotypes, we developed an approach to mapping structural variants that segregate in a population sequenced at low coverage. We avoid calling structural variants directly. Instead, the evidence for a potential structural variant at a locus is indicated by variation in the counts of short-reads that map anomalously to that locus. These structural variant traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study...
February 7, 2017: Genetics
https://www.readbyqxmd.com/read/28162765/mutations-in-bmpr2-are-not-present-in-patients-with-pulmonary-hypertension-associated-with-congenital-diaphragmatic-hernia
#6
Joanne S Chiu, Lijiang Ma, Julia Wynn, Usha Krishnan, Erika B Rosenzweig, Gudrun Aspelund, Marc Arkovitz, Brad W Warner, Foong-Yen Lim, George B Mychaliska, Kenneth Azarow, Robert A Cusick, Dai H Chung, Wendy K Chung
BACKGROUND: Congenital diaphragmatic hernia (CDH) is a prevalent major congenital anomaly with significant morbidity and mortality. Thirty to 40% mortality in CDH is largely attributed to pulmonary hypoplasia and pulmonary hypertension (PH). We hypothesized that the underlying genetic risk factors for hereditary PH are shared with CDH associated PH. METHODS: Participants were recruited as part of the Diaphragmatic Hernia Research & Exploration; Advancing Molecular Science (DHREAMS) study, a prospective cohort of neonates with a diaphragmatic defect enrolled from 2005 to 2012...
January 26, 2017: Journal of Pediatric Surgery
https://www.readbyqxmd.com/read/28157158/epigenetic-alterations-in-parathyroid-cancers
#7
REVIEW
Chiara Verdelli, Sabrina Corbetta
Parathyroid cancers (PCas) are rare malignancies representing approximately 0.005% of all cancers. PCas are a rare cause of primary hyperparathyroidism, which is the third most common endocrine disease, mainly related to parathyroid benign tumors. About 90% of PCas are hormonally active hypersecreting parathormone (PTH); consequently patients present with complications of severe hypercalcemia. Pre-operative diagnosis is often difficult due to clinical features shared with benign parathyroid lesions. Surgery provides the current best chance of cure, though persistent or recurrent disease occurs in about 50% of patients with PCas...
February 1, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28128455/expanding-the-mutation-spectrum-in-icf-syndrome-evidence-for-a-gender-bias-in-icf2
#8
Marlinde L van Boogaard, Peter E Thijssen, Caner Aytekin, Francesco Licciardi, Ayça A Kıykım, Lucia Spossito, Virgil A S H Dalm, Gertjan J Driessen, Rogier Kersseboom, Femke de Vries, Monique M van Ostaijen-Ten Dam, Aydan Ikinciogullari, Figen Dogu, Matias Oleastro, Edgardo Bailardo, Lucia Daxinger, Ercan Nain, Safa Baris, Maarten J D van Tol, Corry Weemaes, Silvère M van der Maarel
Immunodeficiency, centromere instability and facial anomalies (ICF) syndrome is a rare, genetically heterogeneous, autosomal recessive disorder. Patients suffer from recurrent infections caused by reduced levels or absence of serum immunoglobulins. Genetically, four subtypes of ICF syndrome have been identified to date: ICF1 (DNMT3B mutations), ICF2 (ZBTB24 mutations), ICF3 (CDCA7 mutations) and ICF4 (HELLS mutations). In this study we describe seven ICF1 patients and six novel missense mutations in DNMT3B, affecting highly conserved residues in the catalytic domain...
January 27, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28121514/genetic-drivers-of-kidney-defects-in-the-digeorge-syndrome
#9
Esther Lopez-Rivera, Yangfan P Liu, Miguel Verbitsky, Blair R Anderson, Valentina P Capone, Edgar A Otto, Zhonghai Yan, Adele Mitrotti, Jeremiah Martino, Nicholas J Steers, David A Fasel, Katarina Vukojevic, Rong Deng, Silvia E Racedo, Qingxue Liu, Max Werth, Rik Westland, Asaf Vivante, Gabriel S Makar, Monica Bodria, Matthew G Sampson, Christopher E Gillies, Virginia Vega-Warner, Mariarosa Maiorana, Donald S Petrey, Barry Honig, Vladimir J Lozanovski, Rémi Salomon, Laurence Heidet, Wassila Carpentier, Dominique Gaillard, Alba Carrea, Loreto Gesualdo, Daniele Cusi, Claudia Izzi, Francesco Scolari, Joanna A E van Wijk, Adela Arapovic, Mirna Saraga-Babic, Marijan Saraga, Nenad Kunac, Ali Samii, Donna M McDonald-McGinn, Terrence B Crowley, Elaine H Zackai, Dorota Drozdz, Monika Miklaszewska, Marcin Tkaczyk, Przemyslaw Sikora, Maria Szczepanska, Malgorzata Mizerska-Wasiak, Grazyna Krzemien, Agnieszka Szmigielska, Marcin Zaniew, John M Darlow, Prem Puri, David Barton, Emilio Casolari, Susan L Furth, Bradley A Warady, Zoran Gucev, Hakon Hakonarson, Hana Flogelova, Velibor Tasic, Anna Latos-Bielenska, Anna Materna-Kiryluk, Landino Allegri, Craig S Wong, Iain A Drummond, Vivette D'Agati, Akira Imamoto, Jonathan M Barasch, Friedhelm Hildebrandt, Krzysztof Kiryluk, Richard P Lifton, Bernice E Morrow, Cecile Jeanpierre, Virginia E Papaioannou, Gian Marco Ghiggeri, Ali G Gharavi, Nicholas Katsanis, Simone Sanna-Cherchi
Background The DiGeorge syndrome, the most common of the microdeletion syndromes, affects multiple organs, including the heart, the nervous system, and the kidney. It is caused by deletions on chromosome 22q11.2; the genetic driver of the kidney defects is unknown. Methods We conducted a genomewide search for structural variants in two cohorts: 2080 patients with congenital kidney and urinary tract anomalies and 22,094 controls. We performed exome and targeted resequencing in samples obtained from 586 additional patients with congenital kidney anomalies...
February 23, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28111185/novel-frem1-mutations-in-a-patient-with-mota-syndrome-clinical-findings-mutation-update-and-review-of-frem1-related-disorders-literature
#10
REVIEW
Oscar F Chacon-Camacho, Martin Zenker, Denny Schanze, Jasbeth Ledesma-Gil, Juan C Zenteno
Manitoba-oculo-tricho-anal (MOTA) syndrome is an uncommon condition arising from biallelic mutations of FREM1 gene and clinically characterized by a variable spectrum of eyelid malformations, aberrant hairline, bifid or broad nasal tip, and gastrointestinal anomalies. In this report, we describe a patient with a phenotype compatible with MOTA syndrome (aberrant anterior hair line, hypertelorism, unilateral anophthalmia, and bifid and broad nasal tip) in whom two novel FREM1 mutations (c.305 A > G, p.Asp102Gly; and c...
March 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28078310/polg2-deficiency-causes-adult-onset-syndromic-sensory-neuropathy-ataxia-and-parkinsonism
#11
Lionel Van Maldergem, Arnaud Besse, Boel De Paepe, Emma L Blakely, Vivek Appadurai, Margaret M Humble, Juliette Piard, Kate Craig, Langping He, Pierre Hella, François-Guillaume Debray, Jean-Jacques Martin, Marion Gaussen, Patrice Laloux, Giovanni Stevanin, Rudy Van Coster, Robert W Taylor, William C Copeland, Eric Mormont, Penelope E Bonnen
OBJECTIVE: Mitochondrial dysfunction plays a key role in the pathophysiology of neurodegenerative disorders such as ataxia and Parkinson's disease. We describe an extended Belgian pedigree where seven individuals presented with adult-onset cerebellar ataxia, axonal peripheral ataxic neuropathy, and tremor, in variable combination with parkinsonism, seizures, cognitive decline, and ophthalmoplegia. We sought to identify the underlying molecular etiology and characterize the mitochondrial pathophysiology of this neurological syndrome...
January 2017: Annals of Clinical and Translational Neurology
https://www.readbyqxmd.com/read/28076398/identification-of-a-novel-mutation-in-brd4-that-causes-autosomal-dominant-syndromic-congenital-cataracts-associated-with-other-neuro-skeletal-anomalies
#12
Hyun-Seok Jin, Jeonhyun Kim, Woori Kwak, Hyeonsoo Jeong, Gyu-Bin Lim, Cha Gon Lee
Congenital cataracts can occur as a non-syndromic isolated ocular disease or as a part of genetic syndromes accompanied by a multi-systemic disease. Approximately 50% of all congenital cataract cases have a heterogeneous genetic basis. Here, we describe three generations of a family with an autosomal dominant inheritance pattern and common complex phenotypes, including bilateral congenital cataracts, short stature, macrocephaly, and minor skeletal anomalies. We did not find any chromosomal aberrations or gene copy number abnormalities using conventional genetic tests; accordingly, we conducted whole-exome sequencing (WES) to identify disease-causing genetic alterations in this family...
2017: PloS One
https://www.readbyqxmd.com/read/28072960/-novel-compound-heterozygous-tbc1d24-mutations-in-a-boy-with-infantile-focal-myoclonic-epilepsy-and-literature-review
#13
W H Li, S Z Zhou, L M Zhang, X H Wang, Y J Zhang, B B Wu, H J Wang, H W Yang
Objective: To investigate the clinical features and genetic characteristics of patients with TBC1D24 gene mutations. Method: The clinical data of a patient with novel TBC1D24 compound heterozygous mutations from Children's Hospital of Fudan University were collected, the related literature was searched from China National Knowledge Infrastructure, Wanfang Data Knowledge Service Platform, National Center from Biotechnology Information and Pubmed (up to April 2016) by using search terms "TBC1D24" "epilepsy" ...
January 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/28072476/aberrant-right-subclavian-artery-correlation-between-fetal-and-neonatal-abnormalities-and-abnormal-genetic-screening-or-testing
#14
Angela C Ranzini, Francine Hyman, Emily Jamaer, Tim van Mieghem
OBJECTIVES: To determine whether fetuses with an isolated aberrant course of the right subclavian artery (ARSA) have increased risk for chromosomal abnormalities, including trisomy 21 or 22q11 deletion. METHODS: We performed a retrospective chart review of all fetuses with antenatally diagnosed ARSA. Data were collected from fetal anatomic surveys, fetal echocardiograms, noninvasive trisomy 21 screening programs, invasive genetic studies, and neonatal records. RESULTS: Seventy-nine fetuses with ARSA were identified at 20...
January 10, 2017: Journal of Ultrasound in Medicine: Official Journal of the American Institute of Ultrasound in Medicine
https://www.readbyqxmd.com/read/28061824/a-novel-nhs-mutation-causes-nance-horan-syndrome-in-a-chinese-family
#15
Qi Tian, Yunping Li, Rizwana Kousar, Hui Guo, Fenglan Peng, Yu Zheng, Xiaohua Yang, Zhigao Long, Runyi Tian, Kun Xia, Haiying Lin, Qian Pan
BACKGROUND: Nance-Horan Syndrome (NHS) (OMIM: 302350) is a rare X-linked developmental disorder characterized by bilateral congenital cataracts, with occasional dental anomalies, characteristic dysmorphic features, brachymetacarpia and mental retardation. Carrier females exhibit similar manifestations that are less severe than in affected males. METHODS: Here, we report a four-generation Chinese family with multiple affected individuals presenting Nance-Horan Syndrome...
January 7, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28061423/correlation-between-fetal-autopsy-and-prenatal-diagnosis-by-ultrasound-a-systematic-review
#16
REVIEW
A Cristina Rossi, Federico Prefumo
: The objective of this study was to review literature about the correlation between fetal autopsy and ultrasound findings of fetal malformations. Search in PubMed, Medline, EMBASE, Clinicl trials.org, reference list was performed. Inclusion criteria for studies selection were: fetal autopsy performed after termination of pregnancy (TOP) or stillbirth, TOP for fetal anomalies, prenatal diagnosis of malformations, data reported as proportional rates. EXCLUSION CRITERIA: case reports, non English language, data reported in graphs or percentage...
December 29, 2016: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/28057877/previous-miscarriages-and-gli2-are-associated-with-anorectal-malformations-in-offspring
#17
Romy van de Putte, Charlotte H W Wijers, Ivo de Blaauw, Carlo L M Marcelis, Cornelius E J Sloots, Alice S Brooks, Paul M A Broens, Nel Roeleveld, Loes F M van der Zanden, Iris A L M van Rooij
STUDY QUESTION: Are anorectal malformations (ARMs) associated with previous miscarriages or single nucleotide polymorphisms (SNPs) in the Bone Morphogenetic Protein 4 (BMP4) and GLI family zinc finger 2 (GLI2) genes? SUMMARY ANSWER: The SNP rs3738880 in GLI2 and miscarriages were associated with ARM, especially in patients with multiple congenital anomalies (MCA). WHAT IS KNOWN ALREADY: ARM are one of the most common birth defects of the gastrointestinal tract...
January 5, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28054444/heterozygous-pathogenic-variant-in-dact1-causes-an-autosomal-dominant-syndrome-with-features-overlapping-townes-brocks-syndrome
#18
Bryn D Webb, Sanjeeva Metikala, Patricia G Wheeler, Mingma D Sherpa, Sander M Houten, Marko E Horb, Eric E Schadt
A heterozygous nonsense variant was identified in dapper, antagonist of beta-catenin, 1 (DACT1) via whole-exome sequencing in family members with imperforate anus, structural renal abnormalities, genitourinary anomalies, and/or ear anomalies. The DACT1 c.1256G>A;p.Trp419(*) variant segregated appropriately in the family consistent with an autosomal dominant mode of inheritance. DACT1 is a member of the Wnt-signaling pathway, and mice homozygous for null alleles display multiple congenital anomalies including absent anus with blind-ending colon and genitourinary malformations...
January 5, 2017: Human Mutation
https://www.readbyqxmd.com/read/28043400/dental-issues-in-lacrimo-auriculo-dento-digital-syndrome-an-autosomal-dominant-condition-with-clinical-and-genetic-variability
#19
M J Hajianpour, Hannah Bombei, Scott M Lieberman, Rachael Revell, Rachana Krishna, Robert Gregorsok, Simon Kao, Jeff M Milunsky
BACKGROUND AND OVERVIEW: Lacrimo-auriculo-dento-digital (LADD) syndrome is an autosomal dominant disorder with variable lacrimal and salivary gland hypoplasia and aplasia, auricular anomalies and hearing loss, dental defects and caries, and digital anomalies. CASE DESCRIPTION: The authors present the cases of 2 unrelated children with enamel defects and history of dry mouth leading to recurrent dental caries. The referring diagnoses were Sjögren disease and hypohidrotic ectodermal dysplasia, respectively...
December 30, 2016: Journal of the American Dental Association
https://www.readbyqxmd.com/read/28040117/skeletal-dysplasia-with-bowing-long-bones-proposed-flowchart-for-prenatal-diagnosis-with-case-demonstration
#20
Gabriele Tonni, Marcella Palmisano, Mario Lituania, Gianpaolo Grisolia, Ave Maria Baffico, Maria Paola Bonasoni, Pierpaolo Pattacini, Claudio De Felice, Edward Araujo Júnior
OBJECTIVE: Skeletal dysplasia with bowing long bones is a rare group of multiple characterized congenital anomalies. MATERIALS AND METHODS: We introduce a simple, practical diagnostic flowchart that may be helpful in identifying the appropriate pathway of obstetrical management. RESULTS: Herein, we describe four fetal cases of bent bony dysplasia that focus on ultrasound findings, phenotype, molecular tests, distinctive X-ray features, and chondral growth plate histology...
December 2016: Taiwanese Journal of Obstetrics & Gynecology
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