Tag: haplotypes

Nociceptor neurons affect cancer immunosurveillance

Secondary use of biopsies as research specimens The ten melanoma samples used in this study were collected by Sanford Health and classified by a board-certified pathologist. Their secondary use as research specimens (fully de-identified formalin-fixed, paraffin-embedded (FFPE) blocks) was approved under Sanford Health IRB protocol 640 (titled ‘Understanding and improving…

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Leptin receptor co-expression gene network moderates the effect of early life adversity on eating behavior in children

Gillespie, C. F., Phifer, J., Bradley, B. & Ressler, K. J. Risk and resilience: genetic and environmental influences on development of the stress response. Depress Anxiety 26, 984–992 (2009). CAS  PubMed  PubMed Central  Article  Google Scholar  Silveira, P. P. et al. Cumulative prenatal exposure to adversity reveals associations with a…

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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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The determination of the effect(s) of solute carrier family 22-member 2 (SLC22A2) haplotype variants on drug binding via molecular dynamic simulation systems

International Diabetes Federation (IDF). Diabetes Atlas 8th Edition 2017. www.idf.org/our-network/regions-members/africa/welcome.html. Accessed 15 July 2018 (2018). Singh, S., Usman, K. & Banerjee, M. Pharmacogenetic studies update in type 2 diabetes mellitus. World J. Diabetes. 7, 302. doi.org/10.4239/wjd.v7.i15.302 (2016). Article  PubMed  PubMed Central  Google Scholar  Inzucchi, S. E. et al. Management of…

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As of July 2015, the VCFtools project has been moved to github! Please visit the new website here: vcftools.github.io/man_0112a.html

NAME SYNOPSIS DESCRIPTION EXAMPLES BASIC OPTIONS SITE FILTERING OPTIONS INDIVIDUAL FILTERING OPTIONS GENOTYPE FILTERING OPTIONS OUTPUT OPTIONS COMPARISON OPTIONS AUTHOR NAME VCFtools v0.1.12a − Utilities for the variant call format (VCF) and binary variant call format (BCF) SYNOPSIS vcftools [ –vcf FILE | –gzvcf FILE | –bcf FILE]…

Continue Reading As of July 2015, the VCFtools project has been moved to github! Please visit the new website here: vcftools.github.io/man_0112a.html

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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Multidrug resistance microbial therapy | VMRR

Introduction Antimicrobials are the most important and useful therapeutic discovery in the history of medicine. It allows living beings to survive the microbial disease, enhances invasive surgical procedures, ensures animal health, and protects the food chain since 1928 after the discovery of penicillin. However, the indiscriminate use of antibiotics and…

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Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer

Sampson, J. N. et al. Analysis of heritability and shared heritability based on genome-wide association studies for thirteen cancer types. J. Natl Cancer Inst. 107, djv279 (2015). PubMed  PubMed Central  Article  CAS  Google Scholar  Bosse, Y. & Amos, C. I. A decade of GWAS results in lung cancer. Cancer Epidemiol….

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SMAD4 rs10502913 | COPD

1Department of Pulmonary and Critical Care Medicine, Sinopharm Tongmei General Hospital, Datong, People’s Republic of China; 2China-Japan Friendship Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China; 3Department of Emergency, Chinese PLA General Hospital -Fourth Medical Center, Beijing, People’s Republic of China; 4School…

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Protein and functional isoform levels and genetic variants of the BAFF and APRIL pathway components in systemic lupus erythematosus

Pons-Estel, G. J., Ugarte-Gil, M. F. & Alarcón, G. S. Epidemiology of systemic lupus erythematosus. Expert Rev. Clin. Immunol. 13, 799–814 (2017). CAS  PubMed  Article  Google Scholar  Tsokos, G. C. Systemic lupus erythematosus. N. Engl. J. Med. 365, 2110–2121 (2011). CAS  PubMed  Article  Google Scholar  Bossen, C. & Schneider, P….

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Genetic Divergence between auxis thazard and a.rochei based on pcr-rflp analysis of mtdna d-loop region

Tunas of genus Auxis are commercially and ecologically important fish of family Scombridae. There is currently no information concerning the genetic divergence between A. thazard and A. rochei. Therefore, a study was conducted to estimate the degree of genetic divergence between two species based on PCR-RFLP analysis of D -loop…

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Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant

Subjects Normal breast and tumor samples were obtained with the written informed consent from donors and appropriate approval from local ethical committees, with the detailed information described in the respective original publications: normal tissue9, METABRIC14, TCGA35. Differential allelic expression analysis DNA and total RNA from 64 samples of normal breast…

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Genomic Study Reveals Recurrent Inversion Variants, Instability Effects

NEW YORK – A team from Germany, the US, and Italy has tallied recurrent inversions across dozens of human genomes, providing a look at haplotypes containing these polymorphisms, mechanisms that lead to new inversions, and inversion ties to genetic instability and related microdeletion or duplication conditions. The findings appeared in…

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Bioconductor – RAREsim

DOI: 10.18129/B9.bioc.RAREsim     Simulation of Rare Variant Genetic Data Bioconductor version: Release (3.15) Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins – either as provided by default parameters or estimated from…

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Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure

Cattle are among the largest populations of domesticated animals and used as food resources for humans; therefore, their phenotypes and genetic structure have been shaped by artificial selection for human needs and natural adaptation to environmental changes. The phenotypic selection causes genomic changes in breeding traits within breeds, resulting in…

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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Sequencing data We used publicly available sequencing data from the GIAB consortium45, 1000 Genomes Project high-coverage data46 and Human Genome Structural Variation Consortium (HGSVC)4. All datasets include only samples consented for public dissemination of the full genomes. Statistics and reproducibility For generating the assemblies, we used all 14 samples for…

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Genomic Mate Selection version 0.2.0 from GitHub

Predict the usefulness of a cross. Multi-trait selection index mean and variance prediction based on parental haplotypes, a genetic map, and marker effects. Implement cross-validation procedures to estimate the accuracy predicting the performance (breeding value, total genetic value including dominance) of previously unobserved individuals as well as cross means and…

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Nanopore sequencing of the pharmacogene CYP2D6 allows simultaneous haplotyping and detection of duplications.

Liau Y et al. Pharmacogenomics. 2019 Sep; 20(14):1033-1047 doi.org/10.2217/pgs-2019-0080PMID: 31559921 Show Details AbstractAuthors Aim: Long read sequencing offers the promise of overcoming some of the challenges in accurate genotyping of complex genes, along with the advantage of straightforward variant phasing. We have established methods for sequencing and haplotyping of the…

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Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class

Pereira, S. L. Mitochondrial genome organization and vertebrate phylogenetics. Genet. Mol. Biol. 23, 745–752 (2000). CAS  Google Scholar  Boore, J. L. Animal mitochondrial genomes. Nucl. Acids Res. 27, 1767–1780 (1999). CAS  PubMed  PubMed Central  Google Scholar  Formenti, G. et al. Complete vertebrate mitogenomes reveal widespread gene duplications and repeats. BioRxiv…

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Untangling SNP Variations within CYP2D6 Gene in Croatian Roma

CYP2D6 is a highly polymorphic gene whose variations affect its enzyme activity. To assess whether the specific population history of Roma, characterized by constant migrations and endogamy, influenced the distribution of alleles and thus phenotypes, the CYP2D6 gene was sequenced using NGS (Next Generation Sequencing) method-targeted sequencing in three groups…

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South-to-north migration preceded the advent of intensive farming in the Maya region

Moreno-Mayar, J. V. et al. Early human dispersals within the Americas. Science 362, eaav2621 (2018). ADS  PubMed  Google Scholar  Posth, C. et al. Reconstructing the deep population history of Central and South America. Cell 175, 1185–1197.e22 (2018). CAS  PubMed  PubMed Central  Google Scholar  Raghavan, M. et al. Genomic evidence for…

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Color hiring Software Engineer, Bioinformatics in Remote

About Color Color’s mission is to help people lead the healthiest lives that science and medicine can offer. We launched in April 2015 with a simple, affordable genetic test to help people understand their risk for hereditary cancer. In 2017, we added coverage for hereditary heart conditions. Between them, cancer…

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Understanding signatures of positive natural selection in human zinc transporter genes

Datasets and populations We first compiled whole-genome sequencing data to analyze the patterns of variation in ZTGs on two geographical levels. Thus, we explored a worldwide dataset of 2,328 unrelated individuals representing 24 populations across Africa (AFR), Europe (EUR), East Asia (EAS), South Asia (SAS) and America (AMR), denoted as…

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Genetic diversity of common carp (Cyprinus carpio L.) strains breed in Poland based on microsatellite, AFLP, and mtDNA genotype data.

Abstract Abstract The common carp (Cyprinus carpio L.) has a long-standing history in Polish pond aquaculture, which has given rise to a great number of local breeds, strains and hatchery populations. They are well adapted to their local conditions, play an important role for fisherman’s livelihoods and…

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The Clam Cyclina sinensis (Gmelin) Phylogeography Study with 28S rRNA Gene and Potential of Nuclear rRNA Genes in Genetic Assessments of Molluscs

Avise, J. C., 2009. Phylogeography: Retrospect and prospect. Journal of Biogeography, 36: 3–15. Article  Google Scholar  Beheregaray, L. B., 2008. Twenty years of phylogeography: The state of the field and the challenges for the Southern Hemisphere. Molecular Ecology, 17: 3754–3774. Google Scholar  Clement, M., Posada, D., and Crandall, K. A.,…

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Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….

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An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

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Genetic diversity and selection in Puerto Rican horses

Horses have been considered one of our most prized possessions, used for travel, work, food, and pleasure for at least five and a half millennia17,18,19,20. Nevertheless, the ancestry of various horse breeds and their characteristic traits remains unclear21. In this paper, we describe the patterns and the origins of genetic…

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Estimating individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq

doi: 10.1007/s00414-021-02763-0. Online ahead of print. Affiliations Expand Affiliations 1 Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan. hnakani@juntendo.ac.jp. 2 Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan. 3 Department of Forensic Medicine, Juntendo University School of Medicine,…

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GATK GenotypeGVCFs changes HET to REF_ALT

Dear all, I’ve been using GATK HaplotypeCaller / GenotypGVFs (v4.2.3.0) for a while but, recently found something strange. There is a position (7063) with 8 reads (3T + 5A) that, even though HaplotyCaller calls as a HET (see image, lower track): NC_046966.1 7063 . T A,<NON_REF> 177.64 . BaseQRankSum=0.887;DP=8;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.369;RAW_MQandDP=16885,8;ReadPosRankSum=1.345 GT:AD:DP:GQ:PL:SB…

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Very important pharmacogene variants in the Blang population

Introduction The use of drugs should be different among diverse ethnic groups because of differences in ethnicity, age, sex, environmental factors and genetic factors. If these differences are ignored, then drug sensitivity, metabolic rate, and adverse reactions are affected, which influences the curative effect of drugs and aggravates the illness…

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Mitochondrial DNA-like sequences in the human nuclear genome: Characterization and implications in the evolution of mitochondrial DNA

The complete mitochondrial genome of Flustrellidra hispida (Bryozoa, Ctenostomata, Flustrellidridae) was sequenced using a transposon-mediated approach. All but one of the 36 genes were identified (trnS2). The genome is 13,026 bp long, being one of the smallest metazoan mitochondrial genomes sequenced to date with a unique gene order when compared to…

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Ethnic Diversity of DPD activity and the DPYD Gene

Plain Language Summary Fluoropyrimidine (FP; 5-FU, capecitabine) is a common chemotherapy used to treat many different cancers, including cancer of the colon and rectum, upper digestive tract, breast and head and neck. Cancer patients who receive FP chemotherapy are at risk of developing severe side effects from their treatment. A…

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PHG addHapsFromGVCF restart after memory error

PHG addHapsFromGVCF restart after memory error 0 HI there, Thanks for providing this great tool. I’m trying to add Haplotypes using singularity and CreateHaplotypesFromGVCF.groovy Maybe my memory settings are not ideal, after around 100 gvcfs were processed, the script failed because of an out of memory error. Is there a…

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Parallel genomic responses to historical climate change and high elevation in East Asian songbirds

Extreme environments present profound physiological stress. The adaptation of closely related species to these environments is likely to invoke congruent genetic responses resulting in similar physiological and/or morphological adaptations, a process termed “parallel evolution” (1). Existing evidence shows that parallel evolution is more common at the phenotypic level than at…

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GitHub – AI-sandbox/gnomix

This repository includes a python implemenation of Gnomix, a fast and accurate local ancestry method. Gnomix can be used in two ways: training a model from scratch using reference training data or loading a pre-trained Gnomix model (see Pre-Trained Models below) In both cases the models are used to infer…

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selscan not outputting ihs

selscan not outputting ihs 2 Hi all, I’m trying to calculate iHS with selscan: the program seems to apparently run normal, but my output file is empty. I’ve phased my data with SHAPEIT and tried the following commands: selscan –ihs –vcf input.phased.vcf –map input.phased.map –out output.phased selscan –ihs –hap input.phased.haps…

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Genetic basis and adaptation trajectory of soybean from its temperate origin to tropics

Resequencing of soybean accessions from low latitudes To investigate the genomic basis for the natural variation in soybean adaptation to low latitudes, we conducted whole-genome resequencing of a panel of 329 soybean accessions collected from 15 countries and covering all soybean subgroups in which 165 accessions are from in low-latitude…

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Phasing with SHAPEIT

Edit June 7, 2020: The code below is for pre-phasing with SHAPEIT2. For phased imputation using the output of SHAPEIT2 and ultimate production of phased VCFs, see my answer here: A: ERROR: You must specify a valid interval for imputation using the -int argument, So, the steps are usually: pre-phasing…

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Is it possible to report the allele frequency of integer copy numbers >= 3?

Is it possible to report the allele frequency of integer copy numbers >= 3? 0 I am using cn.mops which reports integer CNV for samples (eg CN1, CN3, CN4, CN5, etc.) I hope to report haplotype frequency of detected CNVs, but I am struggling to understand if this is possible….

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Rare variant association analysis (SKAT-O)

Hello everyone, I was wondering if it is statistically acceptable to perform SKAT-O analysis one a single gene. To elaborate, I am looking in a miRNA gene (80nt length) and I have found a small number of rare variants present in my case group, but none in my control group….

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Widespread coexistence of self-compatible and self-incompatible phenotypes in a diallelic self-incompatibility system in Ligustrum vulgare (Oleaceae)

Arista M, Berjano R, Viruel J, Ortiz MÁ, Talavera M, Ortiz P (2017) Uncertain pollination environment promotes the evolution of a stable mixed reproductive system in the self-incompatible Hypochaeris salzmanniana (Asteraceae). Ann Bot 120(3):447–456 CAS  PubMed  PubMed Central  Article  Google Scholar  Barrett SC (2019) ‘A most complex marriage arrangement’: recent…

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PLINK Haplotype blocks estimation not working

Hi, I am using PLINK to estimate haplotype blocks using Gabriel’s method. I am using the following command plink –file Chr$PBS_ARRAY_INDEX –noweb –all –blocks –ld-window-kb 500 And it seemed to be working just fine but when job finished no blocks were called at all. The log file does not mention…

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Insects | Free Full-Text | MtDNA Analysis Indicates Human-Induced Temporal Changes of Serbian Honey Bees Diversity

Local populations of Apis mellifera are rapidly changing by modern beekeeping through the introduction of nonnative queens, selection and migratory beekeeping. To assess the genetic diversity of contemporary managed honey bees in Serbia, we sequenced mitochondrial tRNAleu-cox2 intergenic region of 241 worker bees from 46 apiaries at eight localities. Nine…

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Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates

Feasibility of genomic skimming on the ONT minION sequencer The term ’genomic skimming’ was first coined by in 2012 by Straub et al. (2012)20 as a way to utilize shallow sequencing of gDNA to obtain relatively deeper coverage of high-copy portions of the genome, including mitogenomes. In combining genomic skimming…

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Haplogroup H1e1a

Phylogenetic tree of complete haplogroup H1e1a sequences. Y-DNA Haplogroup R-M207 Summary Haplogroup R is defined by a DNA marker known as M207. Significant frequencies of sub-Saharan L haplogroups (6. Haplogroup H is a human mitochondrial DNA (mtDNA) haplogroup. The report also said 0. Just out of curiosity, I noticed that…

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Strong within-host selection in a maternally inherited obligate symbiont: Buchnera and aphids

Significance Many animals depend on maternally transmitted symbiotic bacteria that provide nutrients or other benefits. The evolution of these symbionts is complicated: natural selection can act on hosts, favoring symbionts that increase host reproduction, or on symbionts, favoring symbionts that spread within hosts. Furthermore, transmission bottlenecks can facilitate the spread…

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