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Omics score: 7

Whole exome sequencing for HELIC

ABSTRACT: The HELIC study has been whole genome sequencing individuals from 2 Greek isolated populations at 1x depth. The genotype calling process crucially involves a VQSR step followed by imputation-based refinement. We have been investigating optimal ways to increase calling accuracy. To aid us in setting appropriate parameters for VQSR and other QC steps, we have carried out whole exome sequencing of a small number of HELIC samples.

PROVIDER: EGAS00001000602 | EGA |

REPOSITORIES: EGA

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EGAS00001000602-sc-20151012 - samples

Project description:The HELIC study has been whole genome sequencing individuals from 2 Greek isolated populations at 1x depth. The genotype calling process crucially involves a VQSR step followed by imputation-based refinement. We have been investigating optimal ways to increase calling accuracy. To aid us in setting appropriate parameters for VQSR and other QC steps, we have carried out whole exome sequencing of a small number of HELIC samples.

| EGAD00001001638 | EGA

15x WGS HELIC MANOLIS

Project description:15x whole genome sequencing in samples from the Cretan Greek isolate collection HELIC MANOLIS

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EGAS00001000067-sc-20151012 - samples

Project description:Whole-genome sequencing at 4x of 250 samples from the Greek isolate collection HELIC

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EGAS00001001207-sc-20160127 - samples

Project description:15x whole genome sequencing in samples from the Cretan Greek isolate collection HELIC MANOLIS

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Low coverage whole genome sequencing of samples from the Cretan Greek isolate collection HELIC MANOLIS

Project description:Whole-genome sequencing at 1x of samples from the Cretan Greek isolate collection HELIC-MANOLIS. Genome-wide association studies of complex traits have been successful in identifying common variant associations, but a substantial heritability gap remains. The field of complex trait genetics is shifting towards the study of low frequency and rare variants, which are hypothesised to have larger effects. The study of these variants can be empowered by focusing on isolated populations, in which rare variants may have increased in frequency and linkage disequilibrium tends to be extended. This work focuses on an isolated population from Crete, Greece. Sequencing is very efficient in isolated populations, because variants found in a few samples will be shared by others in extended haplotype contexts, supporting accurate imputation.

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Illumina ExomeChip genotyping data from the Cretan Greek isolate collection HELIC MANOLIS

Project description:Isolated populations can empower the identification of rare variation associated with complex traits through next generation association studies. Here we have genotyped individuals from a Greek population isolate on the Illumina HumanExome Beadchip. The HELIC (Hellenic Isolated Cohorts) MANOLIS (Minoan Isolates) collection focuses on Anogia and surrounding Mylopotamos villages. Recruitment of this population-based sample was primarily carried out at the village medical centres. All individuals were older than 17 years and had to have at least one parent from the Mylopotamos area. www.helic.org **The data may not be used for population genetics analyses.**

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Illumina Human OmniExpress genotyping data from the Cretan Greek isolate collection HELIC MANOLIS

Project description:Isolated populations can empower the identification of rare variation associated with complex traits through next generation association studies. Here we have genotyped individuals from a Greek population isolate on the Illumina Human OmniExpress BeadChip array. The HELIC (Hellenic Isolated Cohorts) MANOLIS (Minoan Isolates) collection focuses on Anogia and surrounding Mylopotamos villages. Recruitment of this population-based sample was primarily carried out at the village medical centres. All individuals were older than 17 years and had to have at least one parent from the Mylopotamos area. www.helic.org **The data may not be used for population genetics analyses**

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A Genome-Wide Search for Greek and Jewish Admixture in the Kashmiri Population

Project description:The Kashmiri population is an ethno-linguistic group that resides in the Kashmir Valley in northern India. A longstanding hypothesis is that this population derives ancestry from Jewish and/or Greek sources. There is historical and archaeological evidence of ancient Greek presence in India and Kashmir. Further, some historical accounts suggest ancient Hebrew ancestry as well. To date, it has not been determined whether signatures of Greek or Jewish admixture can be detected in the Kashmiri population. Using genome-wide genotyping and admixture detection methods, we determined there are no significant or substantial signs of Greek or Jewish admixture in modern-day Kashmiris. The ancestry of Kashmiri Tibetans was also determined, which showed signs of admixture with populations from northern India and west Eurasia. These results contribute to our understanding of the existing population structure in northern India and its surrounding geographical areas.

2016-08-16 | GSE85594 | GEO

Project description:Greek Vitis

| PRJNA805368 | ENA

Calling Cards: a customizable platform to longitudinally record protein-DNA interactions over time in cells and tissues

Project description:Calling Cards is a platform technology to record a cumulative history of transient protein-DNA interactions in the genome of genetically targeted cell types. The record of these interactions are recovered by next generation sequencing. Compared to other genomic assays, whose readout provides a snapshot at the time of harvest, Calling Cards enables correlation of historical molecular states to eventual outcomes or phenotypes. To achieve this, Calling Cards uses the piggyBac transposase to insert self-reporting transposon (SRT) “Calling Cards” into the genome, leaving permanent marks at interaction sites. Calling Cards can be deployed in a variety of in vitro and in vivo biological systems to study gene regulatory networks involved in development, aging, and disease. Out of the box, it assesses enhancer usage but can be adapted to profile specific transcription factor binding with custom transcription factor (TF)-piggyBac fusion proteins. The Calling Cards workflow has five main stages: delivery of Calling Card reagents, sample preparation, library preparation, sequencing, and data analysis. Here, we first present a comprehensive guide for experimental design, reagent selection, and optional customization of the platform to study additional TFs. Then, we provide an updated protocol for the five steps, using reagents that improve throughput and decrease costs, including an overview of a newly deployed computational pipeline. This protocol is designed for users with basic molecular biology experience to process samples into sequencing libraries in 1-2 days. Familiarity with bioinformatic analysis and command line tools is required to set up the pipeline in a high performance computing environment and to conduct downstream analyses.

2023-02-01 | GSE223926 | GEO

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