Featured Research

from universities, journals, and other organizations

Whole genome or exome sequencing: An individual insight

Date:
June 26, 2013
Source:
BioMed Central Limited
Summary:
Focusing on parts rather than the whole, when it comes to genome sequencing, might be extremely useful, finds new research. The research compares several sequencing technologies in the same individual with Charcot-Marie-Tooth disease (CMT), and shows that sequencing the coding regions alone at high depth of coverage can identify the genetic variation behind this disease, and was also able to resolve previous ambiguities. Next generation sequencing for understanding human DNA variation and genetic disorders is advancing in leaps and bounds.

Focusing on parts rather than the whole, when it comes to genome sequencing, might be extremely useful, finds research in BioMed Central's open access journal Genome Medicine. The research compares several sequencing technologies in the same individual with Charcot-Marie-Tooth disease (CMT), and shows that sequencing the coding regions alone at high depth of coverage can identify the genetic variation behind this disease, and was also able to resolve previous ambiguities.

Next generation sequencing for understanding human DNA variation and genetic disorders is advancing in leaps and bounds. Whole genome sequencing reads all of an individual's DNA, whereas exome sequencing captures only the parts of the DNA which code for proteins. Exome sequencing is faster and cheaper, but concerns have previously been raised that it misses important information.

A team from Baylor College of Medicine led by Prof. James Lupski and Prof. Richard Gibbs compared several different exome and whole genome sequencing technologies on DNA from the same person with CMT. Prof. Jim Lupski explained, "Both methods were able to find the same 12 variants which affect cellular response to specific drugs such as betablockers, warfarin and the anti-cancer drug paclitaxel, and identify novel CMT-associated mutations in SH3TC2 that encodes for a protein with a role in peripheral nerve myelination."

Exome sequencing had fewer false positives, and a greater sensitivity due to the higher coverage achieved when focusing only in a small fraction of the genome. Consequently it was able to correctly identify nucleotides which were ambiguous when using whole genome sequencing at lower coverage, and so clarify whether they were associated with CMT or not.

Prof. Richard Gibbs commented, "The higher coverage afforded by focusing on the exome at approximately 120x for clinical exomes allows greater precision of exome sequencing making this a superior approach, rather than a shortcut, to find which people might respond to a particular therapy or to define who has a specific disease."


Story Source:

The above story is based on materials provided by BioMed Central Limited. Note: Materials may be edited for content and length.


Journal Reference:

  1. James R Lupski, Claudia Gonzaga-Jauregui, Yaping Yang, Matthew N Bainbridge, Shalini Jhangiani, Christian J Buhay, Christie L Kovar, Min Wang, Alicia C Hawes, Jeffrey G Reid, Christine Eng, Donna M Muzny and Richard A Gibbs. Exome sequencing resolves apparent incidental findings and reveals further complexity of SH3TC2 variant alleles causing CMT neuropathy. Genome Medicine, (in press)

Cite This Page:

BioMed Central Limited. "Whole genome or exome sequencing: An individual insight." ScienceDaily. ScienceDaily, 26 June 2013. <www.sciencedaily.com/releases/2013/06/130626211922.htm>.
BioMed Central Limited. (2013, June 26). Whole genome or exome sequencing: An individual insight. ScienceDaily. Retrieved July 23, 2014 from www.sciencedaily.com/releases/2013/06/130626211922.htm
BioMed Central Limited. "Whole genome or exome sequencing: An individual insight." ScienceDaily. www.sciencedaily.com/releases/2013/06/130626211922.htm (accessed July 23, 2014).

Share This




More Health & Medicine News

Wednesday, July 23, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Stone Fruit Listeria Scare Causes Sweeping Recall

Stone Fruit Listeria Scare Causes Sweeping Recall

Newsy (July 22, 2014) The Wawona Packing Company has issued a voluntary recall on the stone fruit it distributes due to a possible Listeria outbreak. Video provided by Newsy
Powered by NewsLook.com
Huge Schizophrenia Study Finds Dozens Of New Genetic Causes

Huge Schizophrenia Study Finds Dozens Of New Genetic Causes

Newsy (July 22, 2014) The 83 new genetic markers could open dozens of new avenues for schizophrenia treatment research. Video provided by Newsy
Powered by NewsLook.com
CDC Head Concerned About a Post-Antibiotic Era

CDC Head Concerned About a Post-Antibiotic Era

AP (July 22, 2014) Sounding alarms about the growing threat of antibiotic resistance, CDC Director Tom Frieden warned Tuesday if the global community does not confront the problem soon, the world will be living in a devastating post-antibiotic era. (July 22) Video provided by AP
Powered by NewsLook.com
Courts Conflicted Over Healthcare Law

Courts Conflicted Over Healthcare Law

AP (July 22, 2014) Two federal appeals courts issued conflicting rulings Tuesday on the legality of the federally-run healthcare exchange that operates in 36 states. (July 22) Video provided by AP
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins