New targeted resequencing technologies and resources for the community

stanford_genome_tech

Junior Member

Join Date: Aug 2009

Posts: 7
- Share
- Tweet
#1

New targeted resequencing technologies and resources for the community

11-16-2011, 05:00 PM

Alternatives to current capture technologies for custom assays

Oligonucleotide Selective sequencing (OS-Seq)
Capture and targeting integrated on the flow cell.

https://www.nature.com/nbt/journal/v29/n11/full/nbt.1996.html

Open source capture resources for in-solution capture including capture oligo sequences across the exome

A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing

https://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021088

We have developed an integrated strategy for targeted resequencing and analysis of gene subsets from the human exome for variants. Our capture technology is geared towards resequencing gene subsets substantially larger than can be done efficiently with simplex or multiplex PCR but smaller in scale than exome sequencing. We describe all the steps from the initial capture assay to single nucleotide variant (SNV) discovery. The capture methodology uses in-solution 80-mer oligonucleotides. To provide optimal flexibility in choosing human gene targets, we designed an in silico set of oligonucleotides, the Human OligoExome, that covers the gene exons annotated by the Consensus Coding Sequencing Project (CCDS). This resource is openly available as an Internet accessible database where one can download capture oligonucleotides sequences for any CCDS gene and design custom capture assays. Using this resource, we demonstrated the flexibility of this assay by custom designing capture assays ranging from 10 to over 100 gene targets with total capture sizes from over 100 Kilobases to nearly one Megabase. We established a method to reduce capture variability and incorporated indexing schemes to increase sample throughput. Our approach has multiple applications that include but are not limited to population targeted resequencing studies of specific gene subsets, validation of variants discovered in whole genome sequencing surveys and possible diagnostic analysis of disease gene subsets. We also present a cost analysis demonstrating its cost-effectiveness for large population studies.

Open source capture oligonucleotides across the genome

http://oligogenome.stanford.edu

In press at Nucleic Acid Research

Last edited by stanford_genome_tech; 11-16-2011, 05:07 PM.
Tags: None

Previous template Next

Recent Advances in Sequencing Analysis Tools

by seqadmin

The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
- Channel: Articles
05-06-2024, 07:48 AM
Essential Discoveries and Tools in Epitranscriptomics

by seqadmin

The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
- Channel: Articles
04-22-2024, 07:01 AM

Topics	Statistics	Last Post
A Closer Look at the Enigmatic Genomes of Oikopleura dioica by seqadmin Started by seqadmin, 05-10-2024, 06:35 AM	0 responses 19 views 0 likes	Last Post by seqadmin 05-10-2024, 06:35 AM
Advanced Epigenome Editing Platform Explores Gene Regulation Mechanisms by seqadmin Started by seqadmin, 05-09-2024, 02:46 PM	0 responses 23 views 0 likes	Last Post by seqadmin 05-09-2024, 02:46 PM
Telomere Maintenance by PARP1: A New Perspective in Cancer Research by seqadmin Started by seqadmin, 05-07-2024, 06:57 AM	0 responses 21 views 0 likes	Last Post by seqadmin 05-07-2024, 06:57 AM
Enhanced Neoantigen Detection: Introducing NeoHunter by seqadmin Started by seqadmin, 05-06-2024, 07:17 AM	0 responses 21 views 0 likes	Last Post by seqadmin 05-06-2024, 07:17 AM

Seqanswers Leaderboard Ad

Announcement

New targeted resequencing technologies and resources for the community

Latest Articles

ad_right_rmr

News