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Tag: haplotypes
The Evolution from HG19 to HG38
Welcome to another blog post! Reference genomes are essential benchmarks of a species’ genome that facilitate the accurate comparison of individual genomes and are crucial tools for identifying genetic variants and diagnosing rare diseases. Here, we will explore the evolution of the human reference genome, focusing on the transition…
A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing
Introduction Short-read metagenomic sequencing is the technique most widely used to explore the natural habitat of millions of bacteria. In comparison with 16S rRNA sequencing, shotgun metagenomic sequencing (MGS) provides sequence information of the whole genomes, which can be used to identify different genes present in an individual bacterium and…
Accurate detection of identity-by-descent segments in human ancient DNA
Ethics No new aDNA data were generated for this study and we only analysed previously published and publicly available aDNA data. Identifying biological kin is a standard analysis in the aDNA field. Permission for aDNA work on the archaeological samples was granted by the respective excavators, archaeologists, curators and museum…
Blazing the trail to empower agrigenomics research and conservation
Sequencing data for a single human genome, at 30× coverage, takes up to 70 gigabytes of storage. Illumina instruments produced 280 million gigabytes of data in 2021 alone, and by 2025, we’ll need storage capacity for 40 billion gigabytes—and that’s just for human genomes. The Genomics & Bioinformatics Service of…
Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma
Whole-genome sequencing (WGS) analysis of early and advanced adenocarcinomas Whole-genome short read and long read sequencing datasets of 76 lung cancer specimens were analyzed. The datasets included newly generated data for 48 early small-sized lung adenocarcinoma cases (collectively called “Early-Ad” hereafter). These cases included 26 AIS (9 and 17 cases…
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…
Chromosome-level genome assembly of the Asian spongy moths Lymantria dispar asiatica
Boukouvala, M. C. et al. Lymantria dispar (L.) (Lepidoptera: Erebidae): Current Status of Biology, Ecology, and Management in Europe with Notes from North America. Insects 13 (2022). Keena M. A., Richards, J. Y. Comparison of Survival and Development of Gypsy Moth Lymantria dispar L. (Lepidoptera: Erebidae) Populations from Different Geographic…
Indigenous Australian genomes show deep structure and rich novel variation
Inclusion and ethics The DNA samples analysed in this project form part of a collection of biospecimens, including historically collected samples, maintained under Indigenous governance by the NCIG11 at the John Curtin School of Medical Research at the Australian National University (ANU). NCIG, a statutory body within ANU, was founded…
Genetic architecture of cardiac dynamic flow volumes
Virani, S. S. et al. Heart disease and stroke statistics-2021 update: a report from the American Heart Association. Circulation 143, e254–e743 (2021). Article PubMed Google Scholar Nauffal, V. et al. Genetics of myocardial interstitial fibrosis in the human heart and association with disease. Nat. Genet. 55, 777–786 (2023). Article CAS …
vcfdist: accurately benchmarking phased small variant calls in human genomes
The affine gap design space for selecting variant representations As demonstrated in Fig. 1, the main issue with a difference-based format such as VCF is that often there are multiple reasonable sets of variant calls that can be used to represent the same final sequence relative to a reference FASTA. Since…
In Order To Live Yeonmi Park Epub Download 419
Preimplantation genetic diagnosis (PGD) has been used in association with ART to analyze the DNA from embryos at the cleavage or blastocyst stage to determine genetic abnormalities (8). Recent techniques isolate a few cells from the trophectoderm that will become placenta or amnion during embryo development. These isolated cells can…
Advanced Emerging Techniques for Forensic DNA Analysis: STRs, SNPs, and mtDNA Analysis
Alshehhi A, Almarzooqi A, Alhammadi K, Werghi N, Tay GK, Alsafar H (2023) Advancement in human face prediction using DNA. Genes (Basel) 14:136. doi.org/10.3390/genes14010136 CrossRef CAS PubMed Google Scholar Amorim A, Fernandes T, Taveira N (2019) Mitochondrial DNA in human identification: a review. PeerJ 7:e7314. doi.org/10.7717/peerj.7314 CrossRef PubMed Central PubMed …
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…
A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes
Friedman-Einat, M. & Seroussi, E. Avian leptin: bird’s-eye view of the evolution of vertebrate energy-balance control. Trends Endocrinol. Metab. 30, 819–832 (2019). Article CAS PubMed Google Scholar International Chicken Genome Sequencing C. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716 (2004)….
Genetic risk converges on regulatory networks mediating early type 2 diabetes
Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006). Article ADS PubMed Google Scholar Halban, P. A. et al. β-cell failure in type 2 diabetes: postulated mechanisms and prospects for prevention and treatment. Diabetes Care…
Chapter 6 GGHH 2023 – notes – Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes
Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes Define an eQTL Summarise the methodology of RNAseq Understand the reason for expressing RNAseq outcomes as transcripts per million (TPM) Explain why patterns of H3K4me3 and H3K27ac can be used as markers of transcriptionally active genes Incorporate this data into a…
Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing
Tsudzuki, M. Mutations of Japanese quail (Coturnix japonica) and recent advances of molecular genetics for this species. J. Poult. Sci. 45, 159–179 (2008). CAS Google Scholar Recoquillay, J. et al. A medium density genetic map and QTL for behavioral and production traits in Japanese quail. BMC Genom. 16, 10 (2015)….
Whole genomes from Angola and Mozambique inform about the origins and dispersals of major African migrations
A novel collection of genomes from Cabinda, Angola and Maputo, Mozambique Genomic DNA was extracted using saliva samples collected with informed consent and sequenced using the Illumina HiSeq X™ platform to an average autosomal read depth of ~12X from 300 individuals sampled in Cabinda and 50 individuals sampled in Maputo…
Population-specific distribution of TPMT deficiency variants
Introduction Thiopurine S-methyltransferase (TPMT) is a cytoplasmic enzyme that catalyzes the S-methylation of purine analogs, including azathioprine, 6-mercaptopurine (6-MP), and thioguanine.1 The metabolism of these drugs results in two types of metabolites: S-methylmercaptopurine and S-methylthioguanine, which are generally described as inactive metabolites, and S-methyl-thioinosine monophosphate, an inhibitor of de novo…
Ancient diversity in host-parasite interaction genes in a model parasitic nematode
Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973). Google Scholar Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569–577 (2002). Article CAS PubMed Google…
Validating a Mitochondrial Sweep Accompanying the Rapid Spread of a Maternally Inherited Symbiont
Maternally inherited symbiotic bacteria that interfere with the reproduction of their hosts can contribute to selective sweeps of mitochondrial haplotypes through hitch-hiking or coordinate inheritance of cytoplasmic bacteria and host mitochondria. …more Maternally inherited symbiotic bacteria that interfere with the reproduction of their hosts can contribute to selective sweeps of…
Whole mitochondrial genome sequencing provides new insights into the phylogeography of loggerhead turtles (Caretta caretta) in the Mediterranean Sea
Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc Avise JC (1986) Mitochondrial DNA and the evolutionary genetics of higher animals. Philos Trans R Soc Lond B 312:325–342. doi.org/10.1098/rstb.1986.0011 Article CAS Google Scholar Baker CS, Steel D, Calambokidis J, Falcone E, González-Peral U, Barlow J,…
ARFID Genes and Environment (ARFID-GEN): study protocol | BMC Psychiatry
Dinkler L, Bryant-Waugh R. Assessment of avoidant restrictive food intake disorder, pica and rumination disorder: interview and questionnaire measures. Curr Opin Psychiatry. 2021;34(6):532–42. Article Google Scholar American Psychiatric Association. Diagnostic and Statistical Manual of Mental Disorders (5th ed.). Arlington, VA: American Psychiatric Publishing; 2013. Thomas JJ, Lawson EA, Micali N, Misra…
mtDNA “Nomenclutter” and its Consequences on the Interpretation of Genetic Data
Abstract Population-based studies of mitochondrial genetic diversity often require the classification of mitochondrial DNA (mtDNA) haplotypes into more than 2000 described haplogroups, and further grouping those into hierarchically higher haplogroups. Such secondary haplogroup groupings (e.g. “macro-haplogroups”) vary across studies, as they depend on the sample quality, technical factors of haplogroup…
Genetic diversity of merozoite surface protein-5 (MSP-5) of Plasmodium vivax isolates from Malaria patients in Iran | BMC Infectious Diseases
The surface proteins of P. vivax merozoites, including MSP-5 can stimulate the human immune system and play an essential role in the invasion of merozoites into the host reticulocytes which are therefore used to make promising vaccines against P. vivax malaria [28, 29]. Therefore, in the first preliminary step to…
Freshers Job Computational Biology Project Opening at IRRI
“Exclusive Opportunity: Launch Your Computational Biology Career at IRRI! Apply Now!” Freshers Job Computational Biology Project Opening at IRRI Executive – Project Associate 1-Computational Biology Company: IRRI – International Rice Research Institute Location: IRRI SAH, Patancheru, Telangana Job Code: RA23_0731 About IRRI: IRRI is a non-profit, non-political organization that conducts…
ImputePipelinePlugin fails when trying to imputing SNPs on a gvcf file.
Hello everyone, I hope you’re doing great. I’m trying to impute a gvcf using a PHG database. As far as I’m concerned and because of the logs (attached here) of the steps 1 and 2 in the PHG Wiki guide, It seems that I have stablished and populated the PHG…
Can hybrid bentgrass provide dollar spot resistance, drought tolerance?
This interspecific hybrid population is a cross between colonial bentgrass BCD and creeping bentgrass Providence, grown in a greenhouse. Photo by Jinyoung Y. Barnaby Colonial bentgrass is a turfgrass species that can be established on grass tennis courts and golf course fairways and used for erosion control (8). Colonial bentgrasses…
Hussman Institute Celebrates Banner Year at Global Human Genetics Conference
By: Lisette Hilton | November 14, 2023 | 9 min. read | Share Miller School-led studies on neurodegenerative disease chosen for platform presentations, poster awards and abstracts at American Society of Human Genetics’ annual meeting. Many of the more than 8,000 international scientists attending the American Society of Human Genetics (ASHG)…
Dryad | Data — DNA sequence data generated using non-invasive feather and eggshell samples from the Grenada Dove for two gene regions: Cyt b and ND2
As an island endemic with a decreasing population, the Critically Endangered Grenada Dove Leptotila wellsi is threatened by accelerated loss of genetic diversity resulting from ongoing habitat fragmentation. Small, threatened populations are difficult to sample directly but advances in molecular methods mean that non-invasive samples can be used. We performed…
Solved A family has 5 children, two of whom are affected
Transcribed image text: A family has 5 children, two of whom are affected with a genetic disease. They were genotyped for 3 different markers that could be detected with restriction enzymes EcoRI, BamHI, and Xbal. All 3 markers are closely linked on chromosome 15. Th RFLP data are shown below,…
Advocating for PCR-RFLP as molecular tool within malaria programs in low endemic areas and low resource settings
Abstract The road to malaria elimination for low- and middle-income countries is paved with obstacles, including the complexity and high costs of advanced molecular methods for genomic analysis. The usefulness of PCR-RFLP as less complex and affordable molecular surveillance tool in low-endemic malaria regions was assessed in a cross-sectional study…
Haplotype and phylogenetic diversity using mitochondrial 12S rRNA gene marker in Bali cattle | Suselowati
Haplotype and phylogenetic diversity using mitochondrial 12S rRNA gene marker in Bali cattle T. Suselowati – Graduate School of Animal Science Faculty, IPB University, Indonesia R. R. Noor – Department of Animal Production and Technology, Faculty of Animal Science, IPB University, Indonesia *J. Jakaria – Department of Animal Production and…
HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases
HLA allele calling from WES HLA-HD was used to call HLA alleles for 454,824 participants at 3-field resolution (representing the allele’s serological specificity, HLA protein, and synonymous variants). We used the UKB whole-genome genotyping (unavailable in 1283 participants) projected on the 1000 Genome reference to estimate genetic ancestry. We found…
Genes | Free Full-Text | Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley
1. Introduction The Antioquia region has played a pivotal role in the pre-Hispanic history of South America, serving as a gateway for the initial human migrations to the continent and as a hub for the development of a sophisticated culture deeply rooted in the utilization of natural resources and advanced…
Resurgence of SARS-CoV-2 Delta after Omicron variant superinfection in an immunocompromised pediatric patient | Virology Journal
Patient history The patient was a school-aged child previously diagnosed with a neuroinflammatory condition initially treated with the IFN-γ blocking antibody emapalumab-Iszg and ongoing therapy with steroids and monthly etoposide. The patient had a history of varicella encephalitis and remained on suppressive valacyclovir therapy. In early January 2022, the child…
A novel tetra-primer ARMS-PCR approach for the molecular karyotyping of chromosomal inversion 2Ru in the main malaria vectors Anopheles gambiae and Anopheles coluzzii | Parasites & Vectors
Loughlin SO. The expanding Anopheles gambiae species complex. Pathog Glob Health. 2020;114:1. Article PubMed PubMed Central Google Scholar Coluzzi M, Sabatini A, Petrarca V, Di Deco MA. Chromosomal differentiation and adaptation to human environments in the Anopheles gambiae complex. Trans R Soc Trop Med Hyg. 1979;73:483–97. Article CAS PubMed Google…
Mouse mm10 chr4:22,481,383-22,489,763 UCSC Genome Browser v455
Custom Tracks Adiposehidedensesquishpackfull Cerebellumhidedensesquishpackfull Cortexhidedensesquishpackfull Liverhidedensesquishpackfull Lunghidedensesquishpackfull Sintesthidedensesquishpackfull Spleenhidedensesquishpackfull mouse_7_core ATAC Adipose Rep1hidedensefull ATAC Adipose Rep2hidedensefull ATAC Cerebellum Rep1hidedensefull ATAC Cerebellum Rep2hidedensefull ATAC Colon Rep1hidedensefull ATAC Colon Rep2hidedensefull ATAC Cortex Rep1hidedensefull ATAC Cortex Rep2hidedensefull ATAC Heart Rep1hidedensefull ATAC Heart Rep2hidedensefull ATAC Liver Rep1hidedensefull ATAC Liver Rep2hidedensefull ATAC…
Hepatozoon spp. infection in wild canids in the eastern United States | Parasites & Vectors
Hepatozoon spp. infections are widespread in wild canids throughout the eastern US. Hepatozoon canis was detected in six states in our study, while H. americanum was restricted to only two states in the south despite evidence that A. maculatum has spread as far north as Delaware [12]. Both foxes and…
IJMS | Free Full-Text | Whole-Genome Sequencing of 502 Individuals from Latvia: The First Step towards a Population-Specific Reference of Genetic Variation
1. Introduction Human population genetics benefitted from the completion of the human genome sequence [1], which was further advanced by creating the reference of global genome variation [2] and, finally, the establishment of regional references assessing fine details of local variation in whole-genome sequences. Although European populations are relatively well…
B cell polygenic risk scores associate with anti-dsDNA antibodies and nephritis in systemic lupus erythematosus
Objective: B cell function and autoantibodies are important in SLE pathogenesis. In this work, we aimed to investigate the impact of cumulative SLE B cell genetics on SLE subphenotype and autoantibody profile. Methods: Female patients with SLE (n=1248) and healthy controls (n=400) were genotyped using Illumina’s Global Screening Array. Two…
[Question]: What does htvc stand for in haplotypecaller – Parabricks 4.2.0-1 – Parabricks
Hi This is with reference to Parabricks 4.2.0-1 – nvcr.io/nvidia/clara/clara-parabricks:4.2.0-1 I want to know what htvc means in haplotypecaller and what does the associated binary at /usr/local/parabricks/binaries//bin/htvc do within the program. I tried searching for documentation around this but could not find any useful information /usr/local/parabricks/run_pb.py haplotypecaller <…..snipped…..> –verbose –x3…
Transfer learning enables predicti … | Article
McInnes G et al. PLoS Computational Biology. 2020 Nov; 16(11):e1008399 doi.org/10.1371/journal.pcbi.1008399PMID: 33137098 Show Details AbstractAuthorsFunding Information Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic gene whose protein product metabolizes more than 20% of clinically used drugs. Genetic variations in CYP2D6 are responsible for interindividual heterogeneity in drug response that can…
Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton
Gene expression atlas in fiber development To uncover the genetic regulation of gene expression in fiber development, we collected 376 diverse G. hirsutum accessions for genome and transcriptome analysis. A total of 13.5 Tb of genome resequencing data were generated, with an average depth of 15.6× (Supplementary Table 1). Accessions were…
Interpretation question regarding vg call result vcf
Thank you so much for creating such an amazing tool. I am currently having difficulty interpreting vcf results from vg call. I currently performed haplotype-resolved genome assembly and created a graph-genome using both haplotypes (HA and HB) via pggb and vg. Afterwards, a variant called vcf was completed through vg…
VG autoindex with pangenome constructed using minigraph-cactus
Dear developers, I am trying to construct a reference pangenome of a fungi species. After successfully constructing my pangenome using minigraph-cactus, I am struggling to add my isolates’ annotations. For some background: We have de novo assembled and annotated 11 isolates and used the current reference (which has a chromosomal…
To genetically characterize Fasciola adult worms
Introduction Fascioliasis is a zoonotic disease of public health significance and a worldwide distribution.1 The causative agents of Fascioliasis are F. hepatica (F. hepatica; temperate liver fluke) and Fasciola gigantica (tropical liver fluke).2,3 Although it has been recognized for centuries, the disease is currently expanding and has a serious impact…
Computational Tools – PacBio
Paraphase Paraphase is a computational tool for variant calling in homologous genes, for either WGS or targeted sequencing. Paraphase was introduced for gene profiling of spinal muscular atrophy (SMA), for which it successfully identified full-length SMN1 and SMN2 haplotypes. This tool is also accessible through our partner platform DNAnexus. This…
Genotyping, sequencing and analysis of 140,000 adults from Mexico City
Recruitment of study participants The MCPS was established in the late 1990s following discussions between Mexican scientists at the National Autonomous University of Mexico (UNAM) and British scientists at the University of Oxford about how best to measure the changing health effects of tobacco in Mexico. These discussions evolved into…
Genetic diversity of hepatitis B virus quasispecies in different biological compartments reveals distinct genotypes
Tong, S. & Revill, P. Overview of hepatitis B viral replication and genetic variability. J. Hepatol. 64(1 Suppl), S4–S16 (2016). Article CAS PubMed PubMed Central Google Scholar Kramvis, A. Genotypes and genetic variability of hepatitis B virus. Intervirol. 57(3–4), 141–150 (2014). Article Google Scholar Cao, L. et al. Coexistence of…
Genetic analysis challenges the presence of Ixodes inopinatus in Central Europe: development of a multiplex PCR to distinguish I. inopinatus from I. ricinus | Parasites & Vectors
Estrada-Peña A, de la Fuente J. Host distribution does not limit the range of the tick Ixodes ricinus but impacts the circulation of transmitted pathogens. Front Cell Infect Microbiol. 2017;7:1–10. doi.org/10.3389/fcimb.2017.00405. Article Google Scholar Al-Khafaji AM, Clegg SR, Pinder AC, Luu L, Hansford KM, Seelig F, et al. Multi-locus sequence…
Determine INDELs number (both classes separately) from reference and graph-based VCF files
Hi there, this is more so of a hint/suggestion post than a real question since I could manage to find some related posts here on Biostars but appreciate a feedback on the procedure/results for the analysis. In principle, I’m trying to compare the bwa-mem_GATK pipeline working on the linear reference…
Assembly and phylogeographical analysis of novel Taenia solium mitochondrial genomes suggest stratification within the African-American genotype | Parasites & Vectors
Genome assembly and annotation Each genome was assembled following a reference-based strategy. To that end, the reads from each sample were trimmed by quality. Phred quality scores before trimming were greater than Q30 (Additional file 1: Table S1) for all samples. Quality-trimmed reads from the Peruvian and Mexican isolates were…
DNA Study Reveals Cryptic New Species of Pangolin
The newly-identified species, Manis mysteria, is the ninth known pangolin species or the fifth Asian one. The Asian mysterious pangolin (Manis mysteria) separated from the Philippine pangolin (shown here) and Malayan pangolin over 5 million years ago. Image credit: Gregg Yan / CC BY-SA 4.0. Pangolins are mammals of the…
Effect of recombination on genetic diversity of Caenorhabditis elegans
Strong correlation exists between recombination rate and abundance and proportion of indels Whole-genome sequence data of many C. elegans wild isolates now exist. These include Illumina paired-end data of over 600 wild isolates by CeNDR, which also obtained first-generation PacBio long-read data of 14 wild isolates. Second-generation PacBio HiFi data20…
Investigating the role of mitochondrial DNA D-loop variants, haplotypes, and copy number in polycystic ovary syndrome: implications for clinical phenotypes in the Chinese population
Background: The presence of genetic variations in mitochondrial DNA (mtDNA) has been associated with a diverse array of diseases. The objective of this study was to examine the correlations between mtDNA D-loop, its haplotypes, and polycystic ovary syndrome (PCOS) in the Chinese population, and the associations between mtDNA D-loop and…
Calculating haplotype and nucleotide diversity with deep amplicon sequencing data
Calculating haplotype and nucleotide diversity with deep amplicon sequencing data 0 Hi, I want have deep amplicon sequencing data (illumina) where I have samples in row and haplotype (both sequences and names) in column and read counts.The dataframe is a CSV format and I have a separate file in fasta…
Rapid emergence and transmission of virulence-associated mutations in the oral poliovirus vaccine following vaccination campaigns
Sample collection During a prospective study of OPV shedding following a National Health Week (NHW) vaccination campaign in Veracruz State, Mexico, we collected 15,331 stool samples over 10 weeks from children receiving the OPV vaccine, household contacts, and community members (Fig. 2). In our previous study of OPV shedding and…
famous h5a1 haplogroup
[90], Matt Lauerbelongs to Y-DNA haplogroupJ2. [Guardian of Ancient Egypt: Studies in Honor of Zahi Hawass [2020] “Maternal and Paternal Lineages in King Tutankhamun’s Family”, Yehia Z. Gad et al.] [80], TheWright Brothersof the United States belonged to Y-DNA haplogroupE1b1b1, subclade E1b1b1a2 (V13). “, “Evidence for Sub-Haplogroup H5 of Mitochondrial…
Chromosome-scale genome sequence of Suaeda gl
image: Genome size estimation and de novo genome assembly of S. glauca. view more Credit: Horticulture Research Recently, a research paper titled “Chromosome-scale genome sequence of Suaeda glauca sheds light on salt stress tolerance in halophytes“, completed by Professor Qin Yuan’s team from the Center for Genomics, Haixia Institute of Science…
Suaeda Glauca Genome Sequence Reveals Halophyte Salt Tolerance
Recently, a research paper titled “Chromosome-scale genome sequence of Suaeda glauca sheds light on salt stress tolerance in halophytes“, completed by Professor Qin Yuan’s team from the Center for Genomics, Haixia Institute of Science and Technology (Future Technology College) at Fujian Agriculture and Forestry University, has been published in the…
Genome-Wide Association Study of Alopecia Areata in Taiwan
Introduction Alopecia areata (AA) is one of Taiwan’s most common autoimmune hair diseases and incidence rate of AA is 0.22%.1–3 The main symptoms of AA are rapid, non-scarring hair loss that affects body hair, facial hair, eyelashes, and brows.1,2 In the United States, the prevalence of AA is estimated to…
Recommended order of operations for identifying the genomic location and copy-number of an insert with a known sequence from WGS Nanopore fastq files
I generated a new transgenic mouse through random multi-copy integration of a 10.316 Kb DNA fragment with a known sequence . We performed WGS using the PromethION flow cell. From the core I received 500+ fastq files that I have subsequently merged. So far I have performed: de novo assembly…
More than a decade of genetic research on the Denisovans
Stoneking, M. An Introduction to Molecular Anthropology (Wiley, 2017). Fuhlrott, J. C. & Schaaffhausen, H. Über die Knochenfunde aus dem Neandertal bei Mettmann. Verhandlungen naturwissenschaftlicher-historischer Ver. preussisch Rheinl. Westfal. Correspondenz-Bl. 14, 50–52 (1857). Google Scholar Meyer, M. et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos…
Association analysis of agronomic traits and construction of genetic networks by resequencing of 306 sugar beet (Beta vulgaris L.) lines
Genome resequencing approach for genotyping 306 sugar beet germplasm resources In this study, we performed high-depth genome-wide resequencing of 306 sugar beet accessions using an Illumina HiSeq 2000 sequencer, obtaining 1977.12 Gb of sequencing data. This collection included 72 endemic accessions from Northeast China (Harbin), 114 endemic accessions from North China…
The genomic footprint of whaling and isolation in fin whale populations
Samples and sequencing Tissue samples from 50 fin whales (Balaenoptera physalus) were collected using a standard protocol to obtain skin biopsies from free-ranging cetacean species, which use a small stainless-steel biopsy dart deployed from a crossbow or rifle73,74. These samples were collected throughout the Eastern North Pacific (ENP; N = 30, represented…
Development and Validation of a D-Loop mtDNA SNP Assay for the Screening of Specimens in Forensic Casework
Abstract The researchers have selected 14 highly discriminatory single nucleotide polymorphisms (SNPs) based on simulations performed by Salas and Amigo (2010) [1] to be typed using SNaPShotTM (Applied Biosystems, Foster City, CA, USA). The assay was validated by typing more than 100 HVS-1/HVS-2 sequenced samples. No differences were observed between…
Diversity and geographic distribution of haplotypes of Dirofilaria immitis across European endemic countries | Parasites & Vectors
Genchi C, Mortarino M, Rinaldi L, Cringoli G, Traldi G, Genchi M. Changing climate and changing vector-borne disease distribution: the example of Dirofilaria in Europe. Vet Parasitol. 2011;176:295–9. Article PubMed Google Scholar Simón F, González-Miguel J, Diosdado A, Gómez PJ, Morchón R, Kartashev V. The Complexity of zoonotic filariasis episystem…
Allogeneic iPSCs Gaining Momentum Due to Ease of Access and Economies of Scale
While autologous iPSC-based cell therapies are patient-specific, allogeneic iPSC-based cell therapies use donor-derived cells as a starting material. In recent years, a greater number of allogeneic iPSC-derived cell therapies are being studied than autologous therapies. One of the advantages of allogeneic therapy is that a large number of doses can…
Inferences from molecular markers with contrasting modes of inheritance
Genetic markers that differ in mode of inheritance and rate of evolution (a sex-linked Z-specific microsatellite locus, five biparentally inherited microsatellite loci, and maternally inherited mitochondrial [mtDNA] sequences) were used to evaluate the degree of spatial genetic structuring at macro- and microgeographic scales, among breeding regions and local nesting populations…
First report of bovine viral diarrhea virus subgenotypes 1d and 1e in southern Chile | Virology Journal
From the 24 antigenically positive serum samples, 12 amplicons were obtained for sequencing procedures. The low recovery of amplicons is probably due to RNA degradation consecutive to the delay between the first analysis of the samples and the reception of them in our laboratories, what led to repeated frozen-thaw cycles…
High quality de novo genome assembly of the non-conventional yeast Kazachstania bulderi describes a potential low pH production host for biorefineries
Phenotypic characteristics of K. bulderi strains at low pH, organic acids, and antimicrobial drugs Since K. bulderi was isolated, only two studies have been conducted to investigate its physiological characteristics (7, 8). This species was shown to be able to grow efficiently at low pHs ranging from 5.0 to 2.5…
Science in Lab | A New Era of NIPT: Non-Invasive Prenatal Testing for Single Gene Disorders
PRESS RELEASE Published September 5, 2023 DNA plays a crucial role in human growth and development. Irreparable DNA damage caused by external environmental factors leads to disease, which may be transmitted to future generations through genetic material. Common genetic disorders in humans can be divided into four broad categories: chromosomal,…
Eimeria zuernii (Eimeriidae: Coccidia): mitochondrial genome and genetic diversity in the Chinese yak | Parasites & Vectors
Eimeria zuernii mitogenome feature The E. zuernii linear mitogenome was 6176 bp in size and encoded three PCGs, cytb, cox1, and cox3, as well as seven interspersed small subunit (SSU) and twelve interspersed large subunit (LSU) rDNA fragments (Fig. 2). No transfer RNAs (tRNAs) were found in the E. zuernii mitogenome, similar…
Single molecule long-read real-time amplicon-based sequencing of CYP2D6: a proof-of-concept with hybrid haplotypes
Abstract CYP2D6 is a widely expressed human xenobiotic metabolizing enzyme, best known for its role in the hepatic phase I cytochrome P450 enzyme system, where it metabolizes ~20% of medications. It is also expressed in other organs including the brain, where its potential role in physiology and mental health traits…
Incorporating Paleogenomes into Evolutionary Genomics Studies
News:Join Our Online Course: Incorporating Paleogenomes into Evolutionary Genomics Studies 0 Dear all, We are excited to invite you to a comprehensive online course that will equip you with the skills to seamlessly integrate ancient DNA data into your evolutionary genomics studies. The “Incorporating Paleogenomes into Evolutionary Genomics Studies” course…
Research Job: Sr Bioinformatics Scientist
About City of Hope City of Hope is an independent biomedical research and treatment organization for cancer, diabetes, and other life-threatening diseases. Founded in 1913, City of Hope is a leader in bone marrow transplantation and immunotherapy such as CAR T cell therapy. City of Hope’s translational research and personalized…
The complete sequence of a human Y chromosome
Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825–837 (2003). Article ADS CAS PubMed Google Scholar Miga, K. H. et al. Centromere reference models for human chromosomes X and Y satellite arrays. Genome Res. 24, 697–707 (2014)….
Genome-wide study of globally distributed respiratory syncytial virus (RSV) strains implicates diversification utilizing phylodynamics and mutational analysis
Phylogenetic and transmission network analysis Phylogenetic and transmission network analyses provide significant insight into the global evolution, geographical spread, and transmission dynamics of RSV-A and RSV-B. We extensively analyzed the evolutionary history of RSV worldwide by utilizing phylogenetic and phylodynamic analyses38 and estimated that RSV-A and RSV-B appeared around 1953…
Determination of Self-(In)compatibility and Inter-(In)compatibility Relationships in Citrus Using Manual Pollination, Microscopy, and S-Genotype Analyses
This protocol provides a rapid method for determining pollen compatibility and incompatibility in citrus cultivars. This technique can efficiently identify the S genotype and accurately identify citrus self-incompatibility, providing necessary information for selecting suitable pollenizer trees. This is a time-efficient, simple, and reliable technique to select the appropriate parents trees…
Phylogenetic and Phylogeographic Relationships of Populations of Meriones tristrami Thomas, 1892 (Rodentia: Gerbillinae) in Turkey as Inferred from Cytochrome-b and RFLP Analysis
Phylogenetic and Phylogeographic Relationships of Populations of Meriones tristrami Thomas, 1892 (Rodentia: Gerbillinae) in Turkey as Inferred from Cytochrome-b and RFLP Analysis Atıf İçin Kopyala YİĞİT N., ÇOLAK E., Markov G., Yigit F. S., ÇOLAK R., ÇETİNTÜRK D., …Daha Fazla ACTA…
‘Precision prescribing could save millions’ :: C+D
In 2022, the NHS spent £9.69 billion on prescribing drugs to patients in England. But ensuring these drugs are truly effective for patients remains a challenge for policy and health decision makers. In fact, 55% of adults are prescribed drugs that may be ineffective for them due to their genetic…
Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers
Pan-cancer WGS data sources GrCh37/hg19 BAM alignments for 2,489 primary tumour and matched normal whole-genome sequencing data were obtained as previously described18. In brief, 989 tumour–normal (T/N) pairs were obtained from The Cancer Genome Atlas (TCGA) Research Network (Genomic Data Commons at portal.gdc.cancer.gov/, accession: phs000178.v11.p8). Additional WGS data were obtained for 874 T/N pairs…
Mitochondrial DNA sequencing of Kehilan and Hamdani horses from Saudi Arabia
doi: 10.1016/j.sjbs.2023.103741. Epub 2023 Jul 20. Affiliations Expand Affiliation 1 Camel Research Center, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia. Item in Clipboard Abdullah Sheikh. Saudi J Biol Sci. 2023 Sep. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1016/j.sjbs.2023.103741. Epub 2023 Jul 20. Affiliation 1…
IRRI Project Associate I – Computational Biology Bioinformatics, Genomics, GWAS
International Rice Research Institute (IRRI) with the support of the Government of India, Ministry of Agriculture, and Farmers’ Welfare has established IRRI-South Asia Regional Centre (ISARC) in Varanasi, Uttar Pradesh. It is a regional facility that supports research collaboration, training, and service provision to institutions, scientists, farmers, and other stakeholders…
Mitochondrial genomic investigation reveals a clear association between species and genotypes of Lucilia and geographic origin in Australia | Parasites & Vectors
Zumpt F. Myiasis in man and animals in the old world. A textbook for physicians, veterinarians and zoologists. London: Butterworth; 1965. Google Scholar Stevens JR, Wall R. Genetic variation in populations of the blowflies Lucilia cuprina and Lucilia sericata (Diptera: Calliphoridae). Random amplified polymorphic DNA analysis and mitochondrial DNA sequences….
Which hg38 file?
I think Devon’s answer is a bit misleading there. There is a wrapper around bwa-mem called bwakit which can handle ALT haplotypes, but this is not the same as bwa-mem and also not extensively used to my knowledge. The take-home message is: Do not use ALT haplotypes unless you are…
The recent introduction of Angiostrongylus cantonensis and its intermediate host Achatina fulica into Guadeloupe detected by phylogenetic analyses | Parasites & Vectors
Cowie RH. Annotated catalogue of species of Angiostrongylus and the related genera Gallegostrongylus, Rodentocaulus and Stefanskostrongylus (Nematoda: Metastrongyloidea, Angiostrongylidae). J Helminthol. 2019;93:389–423. Article PubMed Google Scholar de Almeida LR, de Souza JGR, Santos HA, Torres EJL, Vilela R, do V, Cruz OMS, et al. Angiostrongylus minasensis n. sp.: new species…
Infection of sheep by Echinococcus multilocularis in Gansu, China: evidence from mitochondrial and nuclear DNA analysis | Infectious Diseases of Poverty
Craig PS, Hegglin D, Lightowlers MW, Torgerson PR, Wang Q. Echinococcosis: control and prevention. Adv Parasitol. 2017;96:55–158. Article CAS PubMed Google Scholar Deplazes P, Dinkel A, Mathis A. Molecular tools for studies on the transmission biology of Echinococcus multilocularis. Parasitology. 2003;127(Suppl):S53–61. Article CAS PubMed Google Scholar Deplazes P, Rinaldi L,…
Dissecting human population variation in single-cell responses to SARS-CoV-2
Sample collection The individuals of self-reported African (AFB) and European (EUB) descent studied are part of the EVOIMMUNOPOP cohort18. In brief, 390 healthy male donors (188 AFB and 202 EUB) were recruited between 2012 and 2013 in Ghent (Belgium), thus, before the COVID-19 pandemic. Blood was obtained from the healthy…
VCF file from PHG for loading into BreedBase
I think you’re looking for the PathsToVCFHaplotypesPlugin. This exports diploid or haploid paths to a VCF file with haplotype allele values (Not SNPs). The VCF file is created by first calling HaplotypeGraphBuilderPlugin to create a graph that includes haplotypes based on the user specified methods. This graph is passed along…
Multiple domestications of Asian rice
Doebley, J. F., Gaut, B. S. & Smith, B. D. The molecular genetics of crop domestication. Cell 127, 1309–1321 (2006). Article CAS PubMed Google Scholar Allaby, R. G., Fuller, D. Q. & Brown, T. A. The genetic expectations of a protracted model for the origins of domesticated crops. Proc. Natl…
HISAT2 HLA genotyping errors
HISAT2 HLA genotyping errors 2 Hi,I’m trying to follow the tutorial for HLA typing and assembly in HISAT2 as described at ccb.jhu.edu/hisat-genotype/index.php/Type:HLA using my own RNAseq data. I do everything as described. I have samtools 1.7 installed. I am able to extract my HLA reads. But when I get to…
Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry
Soltis, P. S. & Soltis, D. E. Polyploidy and Genome Evolution (Springer, 2012). Chen, J. Z. & Birchler, J. A. Polyploid and Hybrid Genomics (Wiley-Blackwell, 2013). Ye, C. Y. et al. The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Mol. Plant 13, 1298–1310…
Invasion success of a Lessepsian symbiont-bearing foraminifera linked to high dispersal ability, preadaptation and suppression of sexual reproduction
Simberloff, D. et al. Impacts of biological invasions: What’s what and the way forward. Trends Ecol. Evol. 28, 58–66 (2013). Article PubMed Google Scholar Bellard, C., Cassey, P. & Blackburn, T. M. Alien species as a driver of recent extinctions. Biol. Lett. doi.org/10.1098/rsbl.2015.0623 (2016). Article PubMed PubMed Central Google Scholar …
Hemoglobin O-Arab first-time molecular detection
Introduction Sickle Cell Disease (SCD) Sickle cell disease is an inherited chronic hemolytic anemia whose clinical manifestations arise from the tendency of the hemoglobin (HbS or sickle hemoglobin) to polymerize and deform red blood cells into the characteristic sickle shape.1 Hb S is insoluble and crystallizes in environments with minimal…
Close-kin mark-recapture informs critically endangered terrestrial mammal status
Sampling and tissue collection Christmas Island is a territory of Australia located in the Indian Ocean approximately 380 km south of Java, Indonesia, and 1500 km west of the Australian mainland. It is a small 135 km2 island composed of tertiary limestone overlying volcanic andesite and basalt and its topography consists of…
Liftedover vcf header/contig compatibility
I have a collaborator that has lifted over their hg19 files to hg38 using Crossmap. The first step in the workflow they need to run is a simple bcftools filter for variant quality. They are getting an unknown file type error. Are there any obvious problems with this header that…
Watch: A method for chromosome-level phasing of HiFi assemblies
As more researchers embrace the benefits of PacBio long-read sequencing technology, an expanding community of analysis tool developers has taken shape. Thanks to this growing excitement around PacBio capabilities there are now many excellent workflows available for creating accurate genome assemblies using HiFi reads. Methods that combine HiFi and Hi-C…
Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas
Crosby, A. W. The Columbian Exchange: Biological and Cultural Consequences of 1492 (Praeger, 1972). Google Scholar Ficek, R. E. Cattle, capital, colonization: Tracking creatures of the Anthropocene in and out of human projects. Curr. Anthropol. 60, S260–S271 (2019). Google Scholar Delsol, N. Disassembling cattle and enskilling subjectivities: Butchering techniques and…