Tag: OMIM

Association of PIK3CA Mutation With Pathologic Complete Response and Outcome by Hormone Receptor Status and Intrinsic Subtype in Early-Stage ERBB2/HER2-Positive Breast Cancer | Oncology | JAMA Network Open

Key Points Question  What is the association of PIK3CA mutations, response to therapy, and outcome by hormone receptor (HR) status and intrinsic subtype among patients with ERBB2/HER2-positive early breast cancer (EBC) treated in a clinical trial? Findings  In this cohort study of 184 patients enrolled in the phase 3 trial…

Continue Reading Association of PIK3CA Mutation With Pathologic Complete Response and Outcome by Hormone Receptor Status and Intrinsic Subtype in Early-Stage ERBB2/HER2-Positive Breast Cancer | Oncology | JAMA Network Open

NM_000546.6(TP53):c.743G>A (p.Arg248Gln) AND Lymphoma – ClinVar

NM_000546.6(TP53):c.743G>A (p.Arg248Gln) AND Lymphoma Based on: 1 submission [Details] Record status: current Accession: RCV000790860.7 Allele description NM_000546.6(TP53):c.743G>A (p.Arg248Gln) Gene: TP53:tumor protein p53 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 17p13.1 Genomic location: Preferred name: NM_000546.6(TP53):c.743G>A (p.Arg248Gln) Other names: p.R248Q:CGG>CAG HGVS: NC_000017.11:g.7674220C>T NG_017013.2:g.18331G>A NM_000546.6:c.743G>AMANE SELECT NM_001126112.3:c.743G>A…

Continue Reading NM_000546.6(TP53):c.743G>A (p.Arg248Gln) AND Lymphoma – ClinVar

An FGFR2 mutation as the potential cause of a new phenotype including early-onset osteoporosis and bone fractures: a case report | BMC Medical Genomics

Anamnesis vitae A 13 year old male born was as result of the VII pregnancy, from unrelated parents. Other pregnancies resulted in: I-II silent miscarriage in the second trimester; III – female, born in 2003 (III-3 Fig. 1) that has the following phenotypic features: genu valgum, hip dysplasia, combined thoracolumbar scoliosis,…

Continue Reading An FGFR2 mutation as the potential cause of a new phenotype including early-onset osteoporosis and bone fractures: a case report | BMC Medical Genomics

Genetic basis of osteogenesis imperfecta from a single tertiary centre in South Africa

We used ES, gene panel testing, and a single variant test to achieve a diagnostic yield of 100% for patients with OI in this study. The patient demographic is representative of the Western Cape Province, with Tygerberg Hospital being the largest tertiary referral centre in the province. Since it is…

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Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases | Genome Medicine

Our cohort comprises 34 families in which a presumably autosomal recessive disease defied molecular diagnosis by clinical exome sequencing (short-read sequencing-based) and reanalysis performed on the index individual for each family (Fig. 1). The index patient in each family was subjected to an average of 10 × depth lrWGS except for Family F8602…

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Bioinformatics Engineer – Lifelancer | Career Page

What you will do Work with other engineers and scientists to build Isos platform, applying AI to biological systems. Design, develop and maintain bioinformatics pipelines for the ingestion, management and analysis of biological datasets, especially -omics, imaging, and clinical data. Perform data analysis and data quality assurance according to best…

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OMIM exercise: ECM diseases in humans (10 pts) Use

Transcribed image text: OMIM exercise: ECM diseases in humans (10 pts) Use www.omim.org Find the OMIM pages for each of the diseases and proteins below, and use the references there to answer the questions, as discussed in class. The assignment should be done on paper and turned in inclass by…

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Human hg38 chr6:31,165,200-31,165,800 UCSC Genome Browser v457

     Custom Tracks ac4C-RIP-seq peaks, hESC CTL-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC CTL-2hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-2hidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 Fix Patcheshidedensesquishpackfull p14 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19…

Continue Reading Human hg38 chr6:31,165,200-31,165,800 UCSC Genome Browser v457

Mutational spectrum and phenotypic variability of Duchenne muscular dystrophy and related disorders in a Bangladeshi population

DMD is a degenerative, fatal, and incurable muscular dystrophy that is typically diagnosed between the ages of three and four. Affected boys have increasing muscle weakness and cardiorespiratory and orthopedic complications and are at risk of cognitive, behavioral, and language difficulties30. Suspected cases often undergo DMD gene mutation screening to…

Continue Reading Mutational spectrum and phenotypic variability of Duchenne muscular dystrophy and related disorders in a Bangladeshi population

NM_000391.4(TPP1):c.379C>T (p.Arg127Ter) AND Angelman syndrome – ClinVar

NM_000391.4(TPP1):c.379C>T (p.Arg127Ter) AND Angelman syndrome Based on: 1 submission [Details] Record status: current Accession: RCV001804926.2 Allele description [Variation Report for NM_000391.4(TPP1):c.379C>T (p.Arg127Ter)] NM_000391.4(TPP1):c.379C>T (p.Arg127Ter) Gene: TPP1:tripeptidyl peptidase 1 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 11p15.4 Genomic location: Preferred name: NM_000391.4(TPP1):c.379C>T (p.Arg127Ter) Other names: p.R127*:CGA>TGA…

Continue Reading NM_000391.4(TPP1):c.379C>T (p.Arg127Ter) AND Angelman syndrome – ClinVar

Exome and genome sequencing to unravel the precise breakpoints of partial trisomy 6q and partial Monosomy 2q | BMC Pediatrics

Here, we report a proband with characteristic features of the clinical syndrome, including downward-slanting palpebral fissures; delayed development of bilateral optic nerve hypoplasia; facial deformity with a small mouth, thin lips, micrognathia, and blepharophimosis; short neck; abnormal deciduous teeth; and malformations of the thorax and short ribs. The proband showed…

Continue Reading Exome and genome sequencing to unravel the precise breakpoints of partial trisomy 6q and partial Monosomy 2q | BMC Pediatrics

Structural Variants in gnomAD v4

Today, we are thrilled to announce the release of genome-wide structural variants (SVs) for 63,046 unrelated samples with genome sequencing (GS) data. All site-level information for 1,199,117 high-quality SVs discovered in these samples is browsable in the gnomAD browser (gnomAD SV v4) and downloadable from the gnomAD downloads page. For…

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OBM Genetics | Whole Genome Sequencing in Era of Newborn Screening

Abstract After the completion of the human genome project, there have been many advances in the field of genetics. With next generation sequencing, patients can undergo genomic analysis through whole exome or whole genome testing. These comprehensive tests can shorten the diagnostic odyssey and guide medical management and thereby potentially…

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The status of the human gene catalogue

Understanding our Genetic Inheritance: The US Human Genome Project, The First Five Years 1991-1995 (US Department of Health and Human Services, US Department of Energy, 1990). Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022). Describes the first complete gap-free assembly and annotation of…

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Wide diagnostic and genotypic spectrum in patients with suspected mitochondrial disease | Orphanet Journal of Rare Diseases

Macken WL, Vandrovcova J, Hanna MG, Pitceathly RDS. Applying genomic and transcriptomic advances to mitochondrial medicine. Nat Rev Neurol. 2021;17(4):215–30. doi.org/10.1038/s41582-021-00455-2 Article  PubMed  Google Scholar  Gorman GS, Chinnery PF, DiMauro S, Hirano M, Koga Y, McFarland R, et al. Mitochondrial diseases. Nat Rev Dis Primers. 2016;2(1). doi.org/10.1038/nrdp.2016.80 Barcia G, Assouline…

Continue Reading Wide diagnostic and genotypic spectrum in patients with suspected mitochondrial disease | Orphanet Journal of Rare Diseases

Comparison of BED files

Comparison of BED files 0 Hi, I have bed files of multiple exome capture kits. Now I need to compare these bed files and produce a comparative plots or tables based different parameters like number of genes covered, bases, OMIM, coding regions, exons and so on. Please suggest a way…

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Elucidating the molecular mechanisms underlying anti-inflammatory effects of Morchella esculenta in the arachidonic acid metabolic pathway by network pharmacology and molecular docking

Identification of the anti-inflammatory target of active ingredients in Morchella esculenta The active ingredient of “Morchella esculenta” according to the NPASS database was (E)-Octadec-11-En-9-Yinoic Acid (EOYA) (Fig. 1), numbered NPC179764, with a chemical formula of C18H30O2, and ‘SMILE’ value, CCCCCC/C=C/C#CCCCCCCCC(=O)O. The targets obtained by searching the “EOYA Smile Value” in the…

Continue Reading Elucidating the molecular mechanisms underlying anti-inflammatory effects of Morchella esculenta in the arachidonic acid metabolic pathway by network pharmacology and molecular docking

NM_005546.4(ITK):c.1741C>T (p.Arg581Trp) AND Autoinflammatory syndrome – ClinVar

NM_005546.4(ITK):c.1741C>T (p.Arg581Trp) AND Autoinflammatory syndrome Based on: 1 submission [Details] Record status: current Accession: RCV002263636.3 Allele description [Variation Report for NM_005546.4(ITK):c.1741C>T (p.Arg581Trp)] NM_005546.4(ITK):c.1741C>T (p.Arg581Trp) Gene: ITK:IL2 inducible T cell kinase [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 5q33.3 Genomic location: Preferred name: NM_005546.4(ITK):c.1741C>T (p.Arg581Trp) HGVS:…

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Total Flavonoids of Rhizoma Drynariae Treat Osteoarthritis

Introduction Osteoarthritis (OA) is a common degenerative joint disease characterized by chronic pain and ambulation limitation, affecting about 250 million people worldwide.1 With increased aging population, the OA incidence rapidly increases and OA has become a major cause of disability.2,3 The morbidity of OA is closely related to articular cartilage,…

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Revealing mechanism of Methazolamide for treatment of ankylosing spondylitis based on network pharmacology and GSEA

Braun, J. & Sieper, J. Ankylosing spondylitis. Lancet 369, 1379–1390. doi.org/10.1016/S0140-6736(07)60635-7 (2007). Article  PubMed  Google Scholar  Lai, S. W., Kuo, Y. H. & Liao, K. F. Incidence of inflammatory bowel disease in patients with ankylosing spondylitis. Ann. Rheum. Dis. 80, e144. doi.org/10.1136/annrheumdis-2019-216362 (2021). Article  PubMed  Google Scholar  Bukowski, B. R….

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GATK AnnotateVcfWithBamDepth returns zero DP for all variants in VCF

Dear all, I am using GATK (v4.1.9.0) AnnotateVcfWithBamDepth to get the DP for all variants in ClinVar VCF in a retina RNA-seq BAM file. However, the tool returns zero depth for all variants in the VCF, even though I checked multiple variants in IGV and I saw that they are…

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NM_000379.4(XDH):c.1510A>G (p.Met504Val) AND Hereditary xanthinuria type 1 – ClinVar

NM_000379.4(XDH):c.1510A>G (p.Met504Val) AND Hereditary xanthinuria type 1 Based on: 1 submission [Details] Record status: current Accession: RCV002479628.1 Allele description [Variation Report for NM_000379.4(XDH):c.1510A>G (p.Met504Val)] NM_000379.4(XDH):c.1510A>G (p.Met504Val) Gene: XDH:xanthine dehydrogenase [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 2p23.1 Genomic location: Preferred name: NM_000379.4(XDH):c.1510A>G (p.Met504Val) HGVS: NC_000002.12:g.31375472T>C…

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The value of whole-exome sequencing as a first-tier genetic test in the diagnosis of skin disorders

In a recent article published in BMC Medical Genomics, researchers recruited a cohort of 25 Chinese genodermatoses patients to examine the genetic etiology by whole-exome sequencing (WES). They evaluated the clinical utility of WES as a tool with the potential to expedite the discovery of the genetic variations underlying all skin…

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Identification of two novel variants of the DMD gene

Introduction Duchenne muscular dystrophy (DMD, OMIM#310200) is a severe X-linked recessive, inherited neuromuscular disorder, characterized by rapidly progressive muscle weakness and muscle wasting throughout the body.1 DMD is more common in males than females, with an incidence rate of 1:5000 and 1:50,000,000, respectively.2 Female heterozygotes theoretically have 50% normal cells…

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Use of bioinformatics in genome research in Saudi Arabia

Background Bioinformatics is a new discipline that merges biology, computer science, and information technology. It involves developing and integrating techniques, such as applied mathematics, statistics, computer science, chemistry, and biochemistry, to solve biological problems. Bioinformatics researchers develop and use computing tools to gain more about the life and survival of…

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Genetic Basis of Childrens Congenital Central Hypothyroidism

Chunyun Fu,1,* Jingsi Luo,2,* Jiasun Su,2 Shujie Zhang,2 Qi Yang,2 Yue Zhang2 1Medical Science Laboratory, Children’s Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530003, People’s Republic of China; 2Department of Genetic Metabolism, Children’s Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning,…

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Re-evaluation and re-analysis of 152 research exomes five years after the initial report reveals clinically relevant changes in 18%

Cohort structure We collected sequencing data and information about age, sex, and phenotypes from 152 families (44 simplex with one, 79 multiplex with two, 24 with three, and five with four or more). The cohort characteristics are depicted in Fig. 2A (details in File S2 [12]). Most affected individuals were younger than…

Continue Reading Re-evaluation and re-analysis of 152 research exomes five years after the initial report reveals clinically relevant changes in 18%

Integrated analysis of copy number variation-associated lncRNAs identifies candidates contributing to the etiologies of congenital kidney anomalies

Study design We aimed to investigate the potential contribution of lncRNAs to the pathogenicity of CAKUT associated CNVs. 19 recurrent CAKUT-associated CNVs were identified based on clinical researches of congenital anomalies of the kidney and urinary tracts (CAKUT) cases3,4,12,13 (Table 1). We retrieved lncRNAs located within these genomic regions as candidate…

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Development of High-Resolution Melting Curve Analysis for rapid detection of SEC23B gene mutation causing Congenital Dyserythropoietic Anemia type II in Indian population | Italian Journal of Pediatrics

Congenital dyserythropoietic anemias (CDAs) are a rare and heterogeneous group of disorders. CDAs are characterized by ineffective erythropoiesis, morphological abnormalities of erythroblasts (bi/multinucleated erythroblast, internuclear bridges, erythroid hyperplasia), haemolysis. Depending on erythroid maturation and precursors involved, three major types of CDA (I, II, III) are identified. Other variants of CDA…

Continue Reading Development of High-Resolution Melting Curve Analysis for rapid detection of SEC23B gene mutation causing Congenital Dyserythropoietic Anemia type II in Indian population | Italian Journal of Pediatrics

View genomic variant #0000026722 – MSeqDR-LSDB Mitochondrial Disease Locus Specific Database

View genomic variant #0000026722 Chromosome 9 Allele Unknown Affects function (as reported) Not classified Affects function (by curator) Not classified Type – DNA change (genomic) (Relative to hg19 / GRCh37) g.6605141T>G Published as – GERP – Segregation – DB-ID GLDC_000222 MSCV – dbSNP ID – Frequency – Sources ; clinvar; Reference – Variant remarks – Genetic origin – Variant_disease – Average frequency (large NGS studies) Variant not found in online data…

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Bioinformatics Scientist – GAP Solutions, Inc.

Provide services as a Bioinformatics Scientist in support of the overall functions of the National Human Genome Research Institute (NHGRI) within the National Institutes of Health (NIH). The purpose of this position is to provide bioinformatics related duties to the Cohorts Data Analytics Core. Duties and Responsibilities: Generate and optimize…

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Guidehouse hiring Bioinformatics Scientist in Bethesda, Maryland, United States

Job FamilyBiostatistician (Digital)Travel RequiredNoneClearance RequiredAbility to Obtain Public TrustWhat You Will DoWe are currently searching for a Bioinformatics Scientist to provide bioinformatics related duties to the Cohorts Data Analytics Core. This is a full time, on-site position supporting the NIH office in Bethesda, MD. Optimize and maintain best practice pipelines…

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Axle Informatics hiring Bioinformatics Scientist in Bethesda, Maryland, United States

Axle Informatics is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations nationally and abroad. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques…

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NM_024496.4(IRF2BPL):c.1157C>T (p.Thr386Met) AND Neurodevelopmental disorder with regression, abnormal movements, loss of speech, and seizures – ClinVar

NM_024496.4(IRF2BPL):c.1157C>T (p.Thr386Met) AND Neurodevelopmental disorder with regression, abnormal movements, loss of speech, and seizures Based on: 1 submission [Details] Record status: current Accession: RCV002475523.1 Allele description [Variation Report for NM_024496.4(IRF2BPL):c.1157C>T (p.Thr386Met)] NM_024496.4(IRF2BPL):c.1157C>T (p.Thr386Met) Gene: IRF2BPL:interferon regulatory factor 2 binding protein like [Gene – OMIM – HGNC] Variant type: single nucleotide…

Continue Reading NM_024496.4(IRF2BPL):c.1157C>T (p.Thr386Met) AND Neurodevelopmental disorder with regression, abnormal movements, loss of speech, and seizures – ClinVar

Bioinformatics Engineer II – Hiring Now at Thermo Fisher Scientific in Bangalore

We are on the lookout for a driven Bioinformatics Engineer II to join our exceptional team at Thermo Fisher Scientific in Bangalore.Growing your career as a Full Time Bioinformatics Engineer II is a great opportunity to develop competitive skills.If you are strong in project management, communication and have the right…

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Genetic studies of paired metabolomes reveal enzymatic and transport processes at the interface of plasma and urine

Study design and participants The GCKD study is an ongoing prospective observational study that enrolled 5,217 adult persons with CKD between 2010 and 2012. Patients regularly seen by nephrologists with eGFR between 30 and 60 ml min−1 per 1.73 m2 or eGFR >60 ml min−1 per 1.73 m2 with UACR > 300 mg per g (or urinary protein/creatinine ratio > 500 mg…

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Splitting of VCF file of CSQ field in the INFO column to tabular format.

VCF file will be having seven fixed columns and INFO column. Chromosome, position, ID, ref, alt, qual, filter, and INFO column. This INFO column will be having the variant related information. In the INFO column CSQ field will be having multiple fields – 82 fields fixed with the delimeter “|”…

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Identifying signatures of positive selection in human populations from North Africa

Henn, B. M. et al. Genomic ancestry of North Africans supports back-to-Africa migrations. PLOS Genet. 8, e1002397 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Arauna, L. R. et al. Recent historical migrations have shaped the gene pool of Arabs and Berbers in North Africa. Mol. Biol. Evol. 34, 318–329…

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Pre-test and post-test genetic counseling

Introduction The yield of genetic prenatal diagnosis has been notably improved by introducing whole genome chromosomal microarray (CMA) analysis, which is now recommended in all cases with structural anomalies,1 allowing an additional diagnostic yield as compared to karyotyping of up to 10%.2,3 Moreover, recent data suggest that the expected diagnostic…

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NM_018026.4(PACS1):c.1199+5G>A AND Schuurs-Hoeijmakers syndrome – ClinVar

NM_018026.4(PACS1):c.1199+5G>A AND Schuurs-Hoeijmakers syndrome Based on: 1 submission [Details] Record status: current Accession: RCV002632445.1 Allele description [Variation Report for NM_018026.4(PACS1):c.1199+5G>A] NM_018026.4(PACS1):c.1199+5G>A Gene: PACS1:phosphofurin acidic cluster sorting protein 1 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 11q13.2 Genomic location: Preferred name: NM_018026.4(PACS1):c.1199+5G>A HGVS: NC_000011.10:g.66220796G>A NG_033900.1:g.155444G>A NM_018026.4:c.1199+5G>AMANE…

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Swiss Firm 4bases Bets on NGS Diagnostics With Library Prep Kits, Analysis Pipeline

NEW YORK – As next-generation sequencing has become a routine tool for disease diagnostics, Swiss clinical product manufacturer 4bases is hoping to expand its DNA sequencing test offerings to capture more of the global market. The Manno-based company, which focuses on producing NGS-based diagnostic kits, recently struck a partnership with…

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Analysis of differential gene immune infiltration and clinical characteristics of skin cutaneous melanoma based on systems biology and drug repositioning methods to identify drug candidates for skin cutaneous melanoma

Skin cutaneous melanoma (SKCM) has a low early detection rate and a high mortality rate. There are many problems such as side effects and drug resistance in existing therapeutic drugs. Current studies have confirmed that SKCM pathogenesis-related genes promote the invasion and metastasis of cutaneous melanoma, but their roles in…

Continue Reading Analysis of differential gene immune infiltration and clinical characteristics of skin cutaneous melanoma based on systems biology and drug repositioning methods to identify drug candidates for skin cutaneous melanoma

Human hg38 chr10:21,513,475-21,525,682 UCSC Genome Browser v446

     Seq2science ChIP-seq hub ChIP-seqhidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 updated Fix Patcheshidedensesquishpackfull p14 updated Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19 Diffhidedensesquishpackfull INSDChidedensesquishpackfull LiftOver & ReMaphidedensesquishpackfull LRG Regionshidedensesquishpackfull Mappabilityhideshow Problematic Regionshidedensesquishpackfull new Recomb…

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A Second Family with Myhre Syndrome Caused by the Same Recurrent SMAD4 Pathogenic Variation (p.Arg496Cys)

Introduction: Myhre syndrome (MS; OMIM #139210) is a rare connective tissue disorder presenting with cardiovascular, respiratory, gastrointestinal, and skeletal system findings. Fewer than 100 patients were reported until recently, and all molecularly confirmed cases had de novo heterozygous gain-of-function mutations in the SMAD4 gene. Dysregulation of the TGF-beta signaling pathway…

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NM_000018.4(ACADVL):c.204G>A (p.Ala68=) AND Very long chain acyl-CoA dehydrogenase deficiency – ClinVar

NM_000018.4(ACADVL):c.204G>A (p.Ala68=) AND Very long chain acyl-CoA dehydrogenase deficiency Based on: 1 submission [Details] Record status: current Accession: RCV001989056.2 Allele description [Variation Report for NM_000018.4(ACADVL):c.204G>A (p.Ala68=)] NM_000018.4(ACADVL):c.204G>A (p.Ala68=) Gene: ACADVL:acyl-CoA dehydrogenase very long chain [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 17p13.1 Genomic location: Preferred…

Continue Reading NM_000018.4(ACADVL):c.204G>A (p.Ala68=) AND Very long chain acyl-CoA dehydrogenase deficiency – ClinVar

NM_017654.4(SAMD9):c.3698C>T (p.Ser1233Leu) AND Inborn genetic diseases – ClinVar

NM_017654.4(SAMD9):c.3698C>T (p.Ser1233Leu) AND Inborn genetic diseases Based on: 1 submission [Details] Record status: current Accession: RCV002542603.1 Allele description [Variation Report for NM_017654.4(SAMD9):c.3698C>T (p.Ser1233Leu)] NM_017654.4(SAMD9):c.3698C>T (p.Ser1233Leu) Gene: SAMD9:sterile alpha motif domain containing 9 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 7q21.2 Genomic location: Preferred name: NM_017654.4(SAMD9):c.3698C>T…

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Advantages of genome sequencing in healthcare

Genome sequencing customises diagnostic procedures for diseases at a very nascent stage and provides personalised treatment In 1990, The Human Genome Project was started which took 13 years for sequencing 20,000 genes and to understand the relationship between the genes and their work together. The idea behind genome sequencing is…

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Children | Free Full-Text | Identification of Extremely Rare Pathogenic CNVs by Array CGH in Saudi Children with Developmental Delay, Congenital Malformations, and Intellectual Disability

3.4. Characteristics of Disease-Associated CNVs Investigations with two array-CGH chips (1 × 244 K, n = 11; 2 × 400 K, n = 52) revealed 2537 CNVs, including 1326 CNVs of ≥300 kb and 1211 CNVs of <300 kb. However, only 24 CNVs (from 13 individuals) qualified as causative for…

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Clinical phenotyping and genetic diagnosis of a large cohort of Sudanese families with hereditary spinocerebellar degenerations

Patients recruitment and interviews We included a total of 90 patients from 38 Sudanese families in this study with the following inclusion criteria: 1. Patients presenting with symptoms, signs, and/or history suggestive of SCD. 2. Non-genetic causes that can mimic neurological illnesses that resemble SCD due to pregnancy- or birth-related…

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dbCNV: deleteriousness-based model to predict pathogenicity of copy number variations | BMC Genomics

MacDonald JR, Ziman R, Yuen RK, Feuk L, Scherer SW. The database of genomic variants: a curated collection of structural variation in the human genome. Nucleic Acids Res. 2014;42(Database issue):D986–992. Article  CAS  PubMed  Google Scholar  Zarrei M, MacDonald JR, Merico D, Scherer SW. A copy number variation map of the…

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Bioinformatics – Astrix Technology Group

ROLES / RESPONSIBILITES · Optimize and maintain best practice pipelines to determine Phenotype Risk Score (PheRS) and perform PheWAS, LabWAS, TWAS, and similar analyses. · Use and maintain large-scale genotype and phenotype databases. · Build computable phenotypes for disease, drug effects, and other conditions using combinations of electronic health record…

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The Clinical Diagnostic Utility of Array CGH in Children with Syndromic Microcephaly

Abstract Background: A prospective study using array CGH in children with Syndromic microcephaly from a tertiary pediatric healthcare centre in India. Aim: To identify the copy number variations causative of microcephaly detected through chromosomal array CGH. Patients and Methods: Of the 60 patients, 33 (55%) males and 27 (45%) females…

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The molecular pathology of schizophrenia: an overview of existing knowledge and new directions for future research

Jones HB. Pathology. In: Wexler P. (eds). Information resources in toxicology (Fourth Edition). Academic Press: San Diego, 2009, pp 357–63. Griesinger W. Die Pathologie und therapie der psychischen krankheiten. (Krabbe:Stuttgart, 1861). Kraepelin E. Psychiatrie: ein Lehrbuch für Studierende und Aerzte. (Verlag von Johann Ambrosius Barth:Leipzig, 1899). Jauhar S, Johnstone M,…

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Navigating the Bioinformatics Workflow for Whole Exome Sequencing: A Step-by-Step Guide

Next-generation sequencing (NGS), which makes millions to billions of sequence reads at a fast rate, has greatly sped up genomics research. At the moment, Illumina, Ion Torrent/Life Technologies, 454/Roche, Pacific Bioscience, Nanopore, and GenapSys are all NGS platforms that can be used. They can produce reads of 100–10,000 bp in…

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Nine patients with KCNQ2-related neonatal seizures and functional studies of two missense variants

Patients and clinical data collection The institutional review board of the Faculty of Medicine, Chulalongkorn University approved this study (IRB No. 264/62) which follows the Declaration of Helsinki Guidelines and all subsequent amendments. Written informed consents were obtained from parents or legal guardians of the participants. From June 2016 to…

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NM_001184.4(ATR):c.4820G>A (p.Ser1607Asn) AND not specified – ClinVar

NM_001184.4(ATR):c.4820G>A (p.Ser1607Asn) AND not specified Based on: 1 submission [Details] Record status: current Accession: RCV001821037.3 Allele description [Variation Report for NM_001184.4(ATR):c.4820G>A (p.Ser1607Asn)] NM_001184.4(ATR):c.4820G>A (p.Ser1607Asn) Gene: ATR:ATR serine/threonine kinase [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 3q23 Genomic location: Preferred name: NM_001184.4(ATR):c.4820G>A (p.Ser1607Asn) HGVS: NC_000003.12:g.142512292C>T NG_008951.1:g.71535G>A…

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Lentiviral CFAP52 human shRNA gene Knockdown/Verification Kit -FenicsBIO

Lentiviral CFAP52 human shRNA gene Knockdown/Verification Kit -FenicsBIO The store will not work correctly in the case when cookies are disabled. JavaScript seems to be disabled in your browser. For the best experience on our site, be sure to turn on Javascript in your browser. We use cookies to…

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Traditional Mongolian Medicine Baolier Capsule

Introduction At present, major progress has been made to prevent and treat cardiovascular disease (CVD) through lifestyle changes and drugs, but CVD is still the main cause of death in humans, especially in developed country and developing country.1 It is worth noting that the residual risk of CVD in patients…

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IJMS | Free Full-Text | High-Efficiency CRISPR/Cas9-Mediated Correction of a Homozygous Mutation in Achromatopsia

1. Introduction Achromatopsia (ACHM) is an inherited retinal dystrophy (IRD) affecting approximately 1 in every 30,000 individuals [1,2]. It is an autosomal-recessive disorder associated with a loss of cone photoreceptor function [1,2,3,4]. ACHM usually shows an early onset presenting pendular nystagmus, poor visual acuity, lack of color vision, and photophobia…

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Investigating ultrastructural morphology in… | F1000Research

Introduction MIRAGE syndrome (myelodysplasia, infection, restriction of growth, adrenal hypoplasia, genital (gonadal) phenotypes, and enteropathy) (OMIM: 617053) is a well-established complex multisystem disorder caused by pathogenic gain-of-function variants in the gene SAMD9.1,2 Changes in this gene were first described in 2016 and to date more than 100 affected individuals have…

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Generation of mesenchymal stromal cells from urine-derived iPSCs of pediatric brain tumor patients

Introduction In 2006, there was a breakthrough in the field of regenerative medicine, when Takahashi and Yamanaka developed the technology to transform any somatic cell into a pluripotent stem cell. These reprogrammed cells, called induced Pluripotent Stem Cells (iPSCs), can be generated by ectopic expression of four transcription factors (i.e….

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Variants studied for intestinal disease due to fat malabsorption

If a variant has more than one submission, it may be counted in more than one significance column. If this is the case, the total number of variants will be less than the sum of the other cells. pathogenic likely pathogenic uncertain significance likely benign benign not provided total 59…

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Utilisation of exome sequencing for muscular disorders in Thai paediatric patients: diagnostic yield and mutational spectrum

We performed ES in 43 Thai paediatric patients with MD or CM from 42 unrelated families. Their clinical features and WES data were analysed simultaneously, enabling the correlation of the ES results with other diagnostic modalities. The overall diagnostic yield for ES was 70% (30/43). The most common MD-disease genes…

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org.Hs.eg.db gives more than one ENTREZID for a gene symbol

There is no way to specify the source of gene symbols for an OrgDb. For TEC, one comes from HGNC, and the other comes from OMIM. When we generate the OrgDb packages, we don’t distinguish between sources, as they are all (as far as NCBI is concerned) ‘real’ gene symbols….

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Human hg38 chr19:11,216,461-11,670,150 UCSC Genome Browser v442

     Custom Tracks 1806hidedensefull 468hidedensefull BT20hidedensefull BT474hidedensefull MCF7hidedensefull T47Dhidedensefull    Mapping and Sequencing Base Positionhidedensefull p13 Fix Patcheshidedensesquishpackfull p13 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19 Diffhidedensesquishpackfull INSDChidedensesquishpackfull LiftOver & ReMaphidedensesquishpackfull LRG Regionshidedensesquishpackfull Mappabilityhideshow RefSeq Acchidedensesquishpackfull…

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NM_004429.5(EFNB1):c.128+5G>A AND Craniofrontonasal syndrome – ClinVar

NM_004429.5(EFNB1):c.128+5G>A AND Craniofrontonasal syndrome Based on: 1 submission [Details] Record status: current Accession: RCV001263203.1 Allele description [Variation Report for NM_004429.5(EFNB1):c.128+5G>A] NM_004429.5(EFNB1):c.128+5G>A Gene: EFNB1:ephrin B1 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: Xq13.1 Genomic location: Preferred name: NM_004429.5(EFNB1):c.128+5G>A HGVS: NC_000023.11:g.68829909G>A NG_008887.1:g.5913G>A NM_004429.5:c.128+5G>AMANE SELECT NC_000023.10:g.68049752G>A NM_004429.4:c.128+5G>A This…

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NM_130797.4(DPP6):c.358+30C>T AND not provided – ClinVar

NM_130797.4(DPP6):c.358+30C>T AND not provided Based on: 1 submission [Details] Record status: current Accession: RCV001707448.1 Allele description [Variation Report for NM_130797.4(DPP6):c.358+30C>T] NM_130797.4(DPP6):c.358+30C>T Gene: DPP6:dipeptidyl peptidase like 6 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 7q36.2 Genomic location: Preferred name: NM_130797.4(DPP6):c.358+30C>T HGVS: NC_000007.14:g.154446358C>T NG_033878.2:g.703373C>T NM_001039350.3:c.166+30C>T NM_001290252.2:c.172+30C>T NM_001290253.2:c.358+30C>T…

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Genome-wide identification of disease-causing copy number variations in 450 individuals with anorectal malformations

CNV analysis After the application of quality filter step I (gender mismatch), two patients were excluded. Through step II (call rate <98%), 40 patients were discarded and after step III (exceeded double of standard deviation), 12 more patients were excluded. In the remaining 396 individuals with ARM, a total of…

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UCSC Genome Browser | Encyclopedia MDPI

1. History Initially built and still managed by Jim Kent, then a graduate student, and David Haussler, professor of Computer Science (now Biomolecular Engineering) at the University of California, Santa Cruz in 2000, the UCSC Genome Browser began as a resource for the distribution of the initial fruits of the…

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NM_005445.4(SMC3):c.181C>T (p.Arg61Trp) AND Cornelia de Lange syndrome 3 – ClinVar

NM_005445.4(SMC3):c.181C>T (p.Arg61Trp) AND Cornelia de Lange syndrome 3 Based on: 1 submission [Details] Record status: current Accession: RCV000760292.1 Allele description [Variation Report for NM_005445.4(SMC3):c.181C>T (p.Arg61Trp)] NM_005445.4(SMC3):c.181C>T (p.Arg61Trp) Gene: SMC3:structural maintenance of chromosomes 3 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 10q25.2 Genomic location: Preferred name:…

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NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr) AND Hereditary cancer-predisposing syndrome – ClinVar

NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr) AND Hereditary cancer-predisposing syndrome Based on: 1 submission [Details] Record status: current Accession: RCV001012497.1 Allele description [Variation Report for NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr)] NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr) Gene: SMAD4:SMAD family member 4 [Gene – OMIM – HGNC] Variant type: single nucleotide variant Cytogenetic location: 18q21.2 Genomic location: Preferred name: NM_005359.6(SMAD4):c.1630C>A (p.Pro544Thr) HGVS:…

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Job – Principal Biostistician/Bioinformatics job at Kenya Medical Research

Vacancy title: Principal Biostistician/Bioinformatics [ Type: FULL TIME , Industry: Research , Category: Research ] Jobs at: Kenya Medical Research – KEMRI Deadline of this Job: 06 October 2022   Duty Station: Within Kenya , Kisumu , East Africa SummaryDate Posted: Tuesday, September 20, 2022 , Base Salary: Not Disclosed…

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All transcript variants in gene MAD1L1 – BIPMed SNP Array

Legend Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column’s header and hold it still. Below, a more detailed description is shown per column. Effect: The variant’s effect on the protein’s function, in the format ‘R/C’ where…

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Human hg38 chr7:73,678,750-73,740,129 UCSC Genome Browser v435

Use drop-down controls below and press refresh to alter tracks displayed.Tracks with lots of items will automatically be displayed in more compact modes.    Custom Tracks H3K27ac Meta NeuN SCZhidedensesquishpackfull H3K27ac NeuN SCZ del_CRDhidedensesquishpackfull H3K27ac NeuN SCZ del_CRD_del_peakshidedensesquishpackfull H3K27ac Tissuehidedensesquishpackfull H3K27ac Tissue BDhidedensesquishpackfull H3K27ac Tissue BD del_CRDhidedensesquishpackfull H3K27ac Tissue BD…

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Penetrance of Mendelian Disease Variants Ranges in Heterozygous Carriers

NEW YORK – Using genetic data from the UK Biobank, a team from Brigham and Women’s Hospital, the Broad Institute, Harvard Medical School, and the Massachusetts Institute of Technology has documented various levels of recessiveness for variants previously implicated in Mendelian conditions. “With increasing exome sequencing of population biobank cohorts,…

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Drosophila carrying epilepsy-associated variants in the vitamin B6 metabolism gene PNPO display allele- and diet-dependent phenotypes

Pyridox(am)ine 5′-phosphate oxidase (PNPO; Enzyme Commission Number 1.4.3.5) is a rate-limiting enzyme in the synthesis of vitamin B6 (VB6) (1). Mutations in PNPO can cause neonatal epileptic encephalopathy, a devastating disease that usually leads to death if untreated (2). Recently, PNPO mutations have also been reported in patients with infantile…

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dbSNP – Wikipedia @ WordDisk

The Single Nucleotide Polymorphism Database[1] (dbSNP) is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI). Although the name of the database implies a collection of…

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Summer Intern -Bioinformatics – Roche – Pleasanton

·  Job facts Summer Intern – (Bioinformatics) The Summer @ Roche Intern Program has been developed to provide students with a fun yet rewarding summer through hands-on experience and numerous opportunities to network with other interns as well as employees in the organization. Additionally, we help our students meet their…

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Bioinformatics Scientist – Bethesda | Mendeley Careers

We are currently searching for a Bioinformatics Scientist to provide support services to satisfy the overall operational objectives of the National Human Genome Research Institute (NHGRI), The primary objective is to provide services and deliverables through performance of support services. This opportunity is full-time, and it is on site in…

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benevolentai Senior Bioinformatics Data Scientist in Douglaston, NY | 688499427

With over 35 nationalities and a range of backgrounds represented in our Benevolent team, we aim to build an inclusive environment where our people can bring their authentic selves to work, be respected for who they are and the exceptional work they do. We welcome and actively encourage applications from…

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Ttc30a affects tubulin modifications in a model for ciliary chondrodysplasia with polycystic kidney disease

Significance Cilia are tubulin-based cellular appendages, and their dysfunction has been linked to a variety of genetic diseases. Ciliary chondrodysplasia is one such condition that can co-occur with cystic kidney disease and other organ manifestations. We modeled skeletal ciliopathies by mutating two established disease genes in Xenopus tropicalis frogs. Bioinformatic…

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Transcription Factor Functions

Transcription Factor Functions 1 I have been wondering if there is a database that contains information about whether a transcription factor has a repressive or an activating or a context-dependent function. factor database transcription • 71 views If you performed a whole-genome FIMO scan, selecting those hits that match your…

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