Articles tagged with Haplotypes
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Researchers have developed the Joint Open Genome and Omics Platform 1.0 (JoGo 1.0), which organizes human gene types into four levels based on global frequency. The database catalogs 19,194 human genes with a novel naming system, enabling secure integration of sensitive datasets and linking each gene type to public resources.
Researchers generated high-quality haplotype-resolved assemblies of the MHC region in five widely used tumor cell lines. The studies identified numerous single nucleotide polymorphisms, indels, and structural variants surrounding HLA class I and II genes, providing valuable resources for cancer immunology research.
Researchers developed Variant-aware Cas-OFFinder, a web-based tool that improves CRISPR accuracy by identifying off-target effects across genetic variations. The tool offers a significant step forward in personalized genome editing by incorporating genetic diversity directly into off-target predictions.
A recent study by Tokyo Medical and Dental University researchers suggests that a specific variant of the CARD9 gene prevalent across northern China, Korea, and Japan may have originated from a common ancestor. The c.820dup variant was found to be relatively common in China and has been estimated to be between 2,000 and 4,000 years old...
Researchers at the University of Illinois have identified strong correlations between SARS-CoV-2 cases and deaths, temperature, and latitude. The studies suggest that the virus is genetically encoded to exhibit seasonal behavior, which could be influenced by vaccine design.
A new study finds that modern-day Scottish, Welsh and Northern Irish people share a common genetic heritage with ancient Pictish populations, contradicting long-held assumptions of exotic origins. The research also reveals surprising genetic similarities between Picts and present-day groups in the UK.
Researchers have identified two new feather mite species associated with the endangered Laysan albatross in Japan. The study provides valuable insights into the ecological dynamics of these parasites and their impact on the bird population. The findings highlight the importance of conservation efforts to protect this species.
Researchers used haplotype-based analyses to study the genetic architecture of tomato fruit quality traits, increasing detection power and accuracy. Haplotypes were found to be more powerful than single-marker analysis in identifying marker-trait associations and predicting phenotypes.
An international team sequenced 3,366 chickpea lines from 60 countries, identifying 29,870 genes, including 1,582 novel ones. The study provides a complete picture of genetic variation within chickpea and validated roadmap for improvement.
A high-resolution map of Arab and Middle Eastern population genetics has been unveiled, providing new insights into human history in the region. The study revealed that ancient populations in the Arabian Peninsula played a central role in early human migration out of Africa.
A new study by Professor Danika Bannasch and colleagues reveals that five distinct dog coat patterns have an ancient origin, dating back over 2 million years. The research suggests that lighter coat colors would have been advantageous to an extinct canid ancestor in arctic environments during glaciation periods.
A new study shows that the genetic basis for Chinook salmon migration timing is determined by a single stretch of DNA, making seasonal runs the same fish. The researchers found that the different runs are part of a single diverse population within a drainage basin.
The study found associations between specific single nucleotide polymorphisms (SNPs) and clinical features of follicular lymphoma, including tumor microenvironment composition. The researchers identified key immune-related genes associated with worse survival outcomes in patients treated with rituximab-containing regimens.
Researchers developed a new software tool called WhatsHap polyphase to phase plant genomes in high resolution and with low error margins. The tool solves the problem using a two-phase process and is now available for polyploid organisms, including plants.
A recent study found that genetic variations in a brain-cleansing water channel affect the depth of non-rapid-eye-movement sleep in humans. The study, published in PLOS Biology, suggests that these variations may influence how the body copes with sleep loss and potentially link to Alzheimer's disease progression.
Researchers analyzed DNA haplotypes associated with hereditary prostate cancer (HPC) and found that one mutation increased risk by 22-fold. The study identified 183 variants linked to HPC at genome-wide significance, shedding light on the genetic factors contributing to disease.
SHAPEIT4 is a powerful computer tool that allows researchers to quickly identify haplotypes in hundreds of thousands of unrelated individuals. This enables the analysis of complex traits and disease risk with unprecedented accuracy.
Researchers linked genetic variation in fruit fly mitochondrial genomes to changes in food intake, providing a new tool for studying human metabolic traits. The study used the Drosophila Genetic Reference Panel and identified specific haplotypes associated with increased food consumption.
Researchers have discovered big chunks of ancient Neanderthal and other ancient DNA in the dark centers of human chromosomes, which can be used to study chromosome behavior during cell division and evolutionary descent. The findings also suggest that certain centromere haplotypes may influence differences in sense of smell.
A new variety of zebra chip disease has been identified in potatoes grown in the Klamath Basin of southwestern Oregon, posing a significant threat to local potato production. The disease, caused by Candidatus Liberibacter solanacearum, can result in yield losses of up to 100% and economic damage estimated at millions annually.
Researchers precisely cut a widespread DNA region from the genome using genome editing, revealing its role in cardiovascular disease. The 9p21.3 haplotype causes abnormalities in vascular smooth muscle cells, leading to heart attacks and stroke. This breakthrough may lead to new treatments for millions worldwide.
A natural history study provides the first comprehensive clinical description of spinal muscular atrophy (SMA) within Amish and Mennonite communities, correlating haplotypes and SMN2 copy number with disease severity. The study reveals differences in disease expression and survival between genotypes with varying numbers of SMN2 copies.
Researchers have identified a group of genes strongly related to childhood nephrotic syndrome, an incurable disease with unknown cause. The study found that specific HLA haplotypes are associated with an increased risk of developing the condition.
Researchers identified Nef MY9 and Pol IY11 as immunodominant epitopes for HLA-C*12:02 haplotype, showing its ability to supplement HLA-B's control over HIV-1 replication in infected individuals. The study adds knowledge to the AIDS research puzzle, highlighting a potential protective mechanism against the virus.
Scientists at North Carolina State University have found that small variations in the bellwether gene can significantly affect male fruit fly lifespan, but not female lifespans. The study sheds light on sex-specific differences in lifespan and highlights the importance of metabolic genes.
A study published at UT Southwestern Medical Center identified over 1,000 gene variants linked to systemic lupus erythematosus (SLE), a serious autoimmune disease. The findings support the potential of precision medicine to improve diagnosis and treatment for SLE, which affects nine times more women than men.
The New Guinea flatworm has been found in Florida, marking a significant threat to the US mainland's ecosystem. The invasive species can spread through human agency and infested plants, posing a risk to native snails and other terrestrial molluscs.
A new method using Droplet Digital PCR Technology enables rapid determination of chromosomal phase of allelic markers hundreds of kilobases apart, providing insights into disease cause and severity. This technology overcomes challenges of current phasing methods, allowing researchers to quickly and affordably determine haplotype data.
Researchers used big data from HapMap and 1000 Genomes projects to discover the gephyrin gene's connection to human history and its role in complex neurological diseases. They found a region with rapid evolution after splitting into yin and yang haplotypes, prevalent across different populations.
A study published in PLOS ONE found that long-lived female house mice are less active than shorter-lived counterparts, consuming less food and displaying reactive personality traits. The researchers suggest that life-history theory predicts individuals with greater life expectancy to be more cautious and energy-conserving.
Scientists have identified six basic lines of genetic variation on the horse Y chromosome, revealing a complex history of breeding practices and movement of stallions. The study sheds light on the development of modern sport horses and highlights the influence of ancient stallions like 'Eclipse'.
Scientists at Max Planck Institute for Molecular Genetics in Berlin have decoded a human genome into its molecular haplotypes, revealing the two chromosome sets differ from each other. The comprehensive analysis identified 159 mutated genes with disease-predisposing potential.
A study published in Molecular Biology and Evolution found that non-African populations carry a piece of DNA from Neanderthals, indicating interbreeding between the two species. The genetic variation is present on the X chromosome and has been confirmed through independent analysis.
Researchers found that a specific gene variant, H2 haplotype, protects individuals with a history of child sexual abuse from heavy drinking and alcohol dependence. In contrast, those with the alternate H1 haplotype had three times the risk of heavy drinking and problems. The study suggests a potential target for therapy development.
Recent research on the Cohen Y chromosome reveals that the Jewish priesthood was established by several unrelated male lines. The study, conducted by Michael F. Hammer and colleagues, found that a common male ancestor lived in the Near East around 3,200 years ago, giving rise to distinct lineages among Cohanim Jews.
Research found that IL-1 gene polymorphisms are associated with alcohol dependence in Spanish Caucasian males, particularly those with a certain haplotype. The study suggests a protective effect of this haplotype on better outcomes, highlighting the complex role of genetic factors in AD.
Common genetic variations in nicotine receptors significantly increase the chance of life-long nicotine addiction among European American youth smokers. A study of 2,827 long-term smokers found that those who began smoking before age 17 with a high-risk haplotype had a 1.6- to 5-fold increased risk of heavy nicotine dependence.
Common genetic variations affecting nicotine receptors can significantly increase the risk of lifelong nicotine addiction in European American youth who begin smoking before age 17. The study found that possession of a high-risk haplotype can lead to a 1.6-fold to almost 5-fold increase in risk of heavy smoking as an adult.
Research suggests that Mexican Americans with the H6 haplotype of the CYP2E1 gene are more susceptible to developing alcoholism. The study also found associations between the H6 haplotype and late-age onset of drinking and heavy drinking habits.
Researchers have identified a piece of doggy DNA that reduces growth in small breeds, ensuring they stay small. The study found a haplotype in all breeds of small dogs, suggesting it is a major contributor to body size.
Researchers developed a new method to analyze the MHC of the human genome, enabling the study of complex diseases and transplanted organs. The method may also be useful in studying other gene complexes with variability.
A detailed study of the Major Histocompatibility Complex (MHC) region reveals a region of stability that may have provided protection against infection and disease. The study found over 300 amino acid changing variants, strong candidates for functional studies to understand the role of variation in MHC-associated disease.
Researchers identified a new genetic variation associated with statin response, finding that 9% of African Americans and 0.2% of Caucasians carry the variation. The study suggests that genetic differences may affect cholesterol lowering and cardiovascular outcomes.
Researchers have identified a specific FCGR3A-FCGR3B haplotype associated with an increased risk of developing rheumatoid arthritis. Homozygous individuals with this haplotype are three times more likely to develop RA, and those with the shared epitope protein sequence have a 10 times higher risk.
Researchers used a fast and low-cost computational tool to predict haplotypes from the world's largest genotypes database. The study provides valuable insights into human genetic variation, enabling faster computation of haplotypes and improving disease research.
The study found that muskoxes were genetically more diverse before the Pleistocene/Holocene transition, with extinct haplotypes only found in northern Asia. The authors suggest that reduced genetic variability may have contributed to the extinction of other great mammals like mammoths.
Researchers found that women with breast cancer were less likely to have two versions of the TCATA haplotype, associated with increased IL-10 expression. High levels of IL-10 may be protective against breast cancer due to its anti-angiogenic effects.
Research using mitochondrial DNA identified two distinct populations in Algeria and Morocco as founders of the Gibraltar macaque population. The study found that the Gibraltar macaques retained a surprisingly high level of genetic variability despite long-term isolation.
Researchers found that genetic variation in bitter taste receptors affects how people perceive bitterness, with some having heightened sensitivity and others being insensitive. This study expands our understanding of individual differences in taste perception and may lead to new insights into the role of bitter compounds in human health.
Researchers found that eastern chipmunks in Illinois and Wisconsin descend from ancestors who survived the last North American ice age in isolated forest pockets. These chipmunks migrated south, merging with warmer east and south populations, challenging long-held assumptions about glacier-driven population migrations.
A new study by Ristaino and Kim May identifies the Ia strain of P. infestans, tracing its probable roots to the Andes Mountains in South America. The researchers analyzed 186 specimens from six regions worldwide, confirming 90% were infected with P. infestans.
Cedars-Sinai researchers found a link between lipoprotein lipase (LPL) and insulin resistance in Mexican-Americans. The study used precise diagnostic tests and genetic analysis to identify two LPL haplotypes associated with high or low levels of insulin resistance.
Researchers analyzed participants' CETP genes to find genetic markers for heart disease. They discovered a pattern of gene variations called haplotype, which showed a significant association with the person's response to statin therapy.
A study found that genetic testing can identify HIV patients at risk of a life-threatening hypersensitive reaction to the antiretroviral drug abacavir. Patients with the HLA-B*5701 allele were over 100 times more likely to experience the adverse reaction.
Researchers at Whitehead Institute identify a new gene, IBD5, on chromosome 5 that increases susceptibility to Crohn's disease. The study provides a strong case for building a haplotype map of the human genome, which could make finding disease-causing genes faster and cheaper.