Prior
exome studies of intellectual disability and schizophrenia, the authors note, have turned up sets of genes significantly overlapping those identified in the new ASD study.
Variation and association to diabetes in 2000 full mtDNA sequences mined from
an exome study in a Danish population Li, S., S. Besenbacher, Y. Li, K. Kristiansen et al. 2014.
Not exact matches
In the
study, whole -
exome sequencing and a targeted analysis of 90 genes implicated in heart disease were applied to 419 unrelated SIDS cases.
Using a novel combination of technologies, including trio
exome sequencing of patient / parental DNA and genetic
studies in the tiny larvae of zebrafish, the EuroEPINOMICS RES consortium found that mutations in the gene CHD2 are responsible for a subset of epilepsy patients with symptoms similar to Dravet syndrome — a severe form of childhood epilepsy that is in many patients resistant to currently available anti-epileptic drugs.
To capture uncommon genetic variants, the
study used an
exome genotyping array to genotype 7,060 epithelial ovarian cancer (EOC) cases and 6,712 cancer - free women from the Ovarian Cancer Association Consortium.
Without the Ludwig money, the Hopkins group would not have been able to do the cancer genetics
studies they're famous for, he notes — for example, the duo has used
exome surveys to identify genes associated with colon and breast cancers.
And she worked with the CLINSEQ
Study, investigating the experiences of patients who were having their
exome sequenced and how they responded to receiving genomic information.
The new
study, which was recently posted to a preprint repository but has not yet been published in a peer - reviewed publication, was the result of researchers comparing the parts of the genome known as
exomes, which code for proteins, from 60,000 people — 10 times more than had ever been attempted.
Even so, Goldstein is quick to point out that 3230 is not the complete set of essential genes in the human body and that only by
studying more
exomes will researchers be able to refine that number.
The
study compared whole -
exome sequencing data from 19 patient samples of mucosal melanoma to 135 samples of sun - exposed melanoma.
The
study used whole -
exome sequencing to characterize genetic alterations that occur at the single nucleotide level for all genes in 25 cell lines commonly used as models of bladder cancer.
«For our
study, we examined 19 autonomous adenomas using whole
exome sequencing,» Calebiro describes their approach.
«They're doing 50 genes rather than a whole
exome» for a gene sequencing
study.
«To date we have over 350 phenotypes enrolled in our
study with over 3,200 patient samples having undergone
exome sequencing.
The Yale - led
study performed whole
exome sequencing ¬ — a technique for sequencing all the expressed genes in a genome ¬ — on TNBC tumors to identify mutations in specific genes or pathways that may indicate response or resistance to the standard of care, which is anthracycline / taxane (ACT) chemotherapy.
That's about 2000 years earlier than suggested by previous
studies focusing on a different, more selective set of genes known as the
exome, but it's in line with recent archaeological findings that point to distinctly Tibetan permanent settlements appearing between 3600 and 5200 years ago, Yang says.
The freely - available software package, MendelScan, is designed to help researchers score and prioritize candidate variants in family
exome sequencing
studies of Mendelian disease.
My first post in 2015 was uncannily prescient: it reviewed a
study that uncover rare variants associated with myocardial infarction using
exome data from NHLBI's Exome Sequencing Project (
exome data from NHLBI's
Exome Sequencing Project (
Exome Sequencing Project (ESP).
Another collaboration was unfolding among the cancer geneticists, sequencing experts, clinical researchers, and surgical oncologists at Johns Hopkins, MD Anderson, and Baylor College of Medicine to
study 32 pairs of head and neck tumor and normal tissue samples by whole -
exome sequencing and validate the findings in an additional 88 samples.
The ESP was a pioneering effort in many ways, and its database of coding variation from thousands of
exomes has been a critical resource for many research
studies.
As a result, we're seeing
exome and genome sequencing
studies published all over the place, not just in genetics / genomics journals but also many that focus on specific tissues (e.g. blood) or diseases (e.g. cancer, metabolic diseases, vision disorders, you name it).
Grandis and Garraway decided to
study a University of Pittsburgh collection of 74 pairs of tumor and normal tissue samples using the Broad's capacity to perform whole -
exome sequencing.
As a follow - up to my previous post, Disease - causing Mutations Discovered by NGS in 2011, I've attempted to compile cancer genome and
exome sequencing
studies published last year.
Very recently, a rather limited number of retrospective
studies, utilizing whole genome sequencing (Talkowski et al., 2012) or whole
exome sequencing (WES) in small cohorts of neonates and aborted fetuses with various ultrasound and / or post-mortem structural abnormalities (Carss et al., 2014; Drury et al., 2015; Alamillo et al., 2015; Westerfield et al., 2015), provided initial proof - of - principle of large - scale prenatal next generation sequencing (NGS).
He noted that there are some ongoing
studies that may further inform this difference in the future, including tumor DNA analysis with whole
exome sequencing and tumor RNA analysis with RNAseq, evaluation of circulating cell - free tumor DNA, and hypermethylation.
Ongoing T2D research activities at CRGGH include 1) whole -
exome sequencing of African families with at least four affected members (data generation is complete and analysis is ongoing), 2) GWAS of 1,200 cases and 1,200 controls from West Africa using the new and more efficient African - centric Affymetrix Axiom genome - wide array with more than 2 million markers, and 3) whole genome expression analysis on skeletal muscle obtained from biopsy from 45 subjects (expression QTL (eQTL)
studies on the dataset are complete).
The literature is afloat in «little hits» from GWAS and / or
exome sequencing
studies.
Exome sequencing
studies of several...
Melanoma was another cancer type surveyed by multiple
exome sequencing
studies in 2011.
In the current
study, Christian Fuchsberger and his 300 + co-authors used a combination of genome sequencing,
exome sequencing, genotyping, and imputation to examine the genetic architecture of type II diabetes.
As you probably know, I'm a fan of
exome sequencing, particularly for
studies of rare inherited disorders.
At the time, they'd already sequenced and analyzed the patient's
exome as part of the
study.
Follow - up of these
studies, including work on long and short non-coding RNA and whole -
exome sequencing, are performed using next - generation sequencing technology.
Notably, that GWAS was conducted using a custom high - throughput SNP array with classic GWAS variants (tag SNPs), a catalog of known protein - altering variants (
exome chip) and several custom sets based on prior
studies of AMD:
In
exome sequencing
studies of Mendelian disorders, any variant already present in dbSNP was usually common, and therefore unlikely to cause rare genetic diseases.
An open - source C / C + + library of analytical tools for human genetic variation data from whole -
exome and whole - genome
studies.
A cohort like the one in the AMD
study (44,000 samples) probably costs $ 2.2 million to genotype, compared to sequencing costs of $ 9.7 million (
exome) to $ 45 million (whole genome).
Microarray
studies and, more recently,
exome sequencing have demonstrated the importance of de novo copy number variations (CNVs) and single - nucleotide variations (SNVs) in ID, but the majority of cases remains undiagnosed.
«We started with candidate gene
studies, then moved to common variants and genome wide association
studies, and then, most recently, leveraged
exome sequencing, he said.
An
exome sequencing
study of Moebius syndrome including atypical cases reveals an individual with CFEOM3A and amutation.
The authors combined
exome sequencing data from 10,437 individuals representing five ancestry groups (European, South Asian, East Asian, Hispanic, and African American) with equivalent data from the WGS
study for a joint dataset comprising 12,940 individuals.
This is a landmark
study not only due to the size, but the systematic characterization of each case using whole - genome sequencing (WGS),
exome sequencing (WES), and transcriptome sequencing (RNA - seq).
In this
study we aim to identify new genetic causes of PCG and JOAG using the newest genetic technologies (
exome sequencing) in families, and to evaluate the role of such new genes in POAG patients.
With support from the Air Force, and in collaboration with military medicine colleagues, he is conducting an
exome sequencing implementation
study in active duty military personnel (MilSeq Project).
His talk covered three very different applications of next - generation sequencing: high - throughput mutational
studies of core promoters, sub-assembly of Illumina reads to 454 - length contigs, and
exome capture to unravel Mendelian disorders.
If they aren't, then the true discovery rate for WGS in
exome - negative cases in this
study is 20 %.
Capitalizing on our experiences with high - profile clinical trials such as the MedSeq Project and BabySeq Project and our strong relationship with the Laboratory for Molecular Medicine, our group is using a combination of modeling and clinical
studies to examine the costs and consequences of integrating genome and
exome sequencing into a variety of clinical settings.
This
study did not disappoint: 650 of 722 cases underwent WGS, with the remaining 72 getting
exome only.
This month in Nature, a group from Jay Shendure's lab reported perhaps the most ambitious targeted resequencing
study to date — the whole
exome sequences of 12 individuals.
In this
study, whole -
exome sequencing was conducted in 10,500 of these participants.