We use cookies to understand how you use our site and to improve your experience. This includes personalizing content and advertising. To learn more, click here. By continuing to use our site, you accept our use of cookies. Cookie Policy.

Features Partner Sites Information LinkXpress
Sign In
Advertise with Us

Download Mobile App

Hybrid Gene Mapping Approach Yields Reference Quality Results

By LabMedica International staff writers
Posted on 15 Jul 2015
Print article
Image: The automated, benchtop Irys instrument enables the genomic researcher to acquire high-resolution, multi-color images and conduct single-molecule analysis of long DNA molecules (Photo courtesy of BioNano Genomics).
Image: The automated, benchtop Irys instrument enables the genomic researcher to acquire high-resolution, multi-color images and conduct single-molecule analysis of long DNA molecules (Photo courtesy of BioNano Genomics).
A team of genomics researchers from the USA and Europe have developed a new approach for describing nearly complete genomes by combining high-throughput DNA sequencing with genome mapping techniques.

Conventional next-generation sequencing (NGS) techniques are able to accurately detect certain types of variation, such as single nucleotide variants and small insertions or deletions, but miss many large or complex forms of genomic variation that are associated with human disease.

To overcome the inherent limitations of existing NGS methods, investigators at the Icahn School of Medicine at Mount Sinai (New York, NY, USA), several other American research institutions, and the European Molecular Biology Laboratory (Hamburg, Germany) combined two single molecule approaches. These were the long read sequencing method from Pacific Biosciences (Menlo Park, CA, USA) and Nanochannel Array and Irys reader technology from BioNano Genomics (San Diego, CA, USA). Pacific Biosciences sequencing enables reads exceeding 10 kilobases in length, which can directly resolve and phase complex forms of variation. The NanoChannel Array method confines and linearizes DNA molecules up to megabases in length to provide high-resolution genome maps.

The two techniques were combined into a hybrid approach that was used to analyze the NA12878 diploid genome, a well-sequenced specimen that is included in the 1000 Genomes project and is often used for benchmarking new techniques.

The investigators reported in the June 29, 2015, online edition of the journal Nature Methods that the hybrid assembly method markedly improved upon the contiguity observed from traditional shotgun sequencing approaches. They were able to identify complex structural variants (SVs) missed by other high-throughput approaches. In addition, they phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies.

“We created a high-throughput strategy that builds highly contiguous de novo genomes without the need for complex jumping libraries or targeted approaches. This strategy, in some cases, automatically resolved complete arms of chromosomes,” said senior author Dr. Ali Bashir, assistant professor of genetics and genomics at the Icahn School of Medicine. “While we focused this study on a human genome, the method can be applied to any new genome, including those with high genomic complexity, such as plants, that have been extremely challenging to study.”

“The study revealed an unprecedented view of genomic complexity, in many cases identifying regions overlooked by conventional sequencing or further refining previously known genetic variant classes,” said contributing author Dr. Jan Korbel, group leader at the European Molecular Biology Laboratory.

Related Links:

Icahn School of Medicine at Mount Sinai
European Molecular Biology Laboratory
BioNano Genomics 

Gold Supplier
SARS-CoV-2 qRT-PCR IVD Reagent Kit
Atomic Fluorescence Spectrometer
POC RT-PCR COVID-19 Testing Platform
Convergys POC RT-PCR COVID-19 Testing Platform
Portable Tube Luminometer
Junior LB 9509

Print article
IIR Middle East


Molecular Diagnostics

view channel

Point-of-Care Lateral Flow Test Detects Bladder Cancer Using Urine Sample within Minutes

A breakthrough diagnostics platform uses a multiplexed lateral flow assay that detects 10 bladder cancer biomarkers from a urine sample in either laboratory or point-of-care settings. SCIENION (Berlin,... Read more


view channel
Image: Bone marrow aspirate from a patient with Acute Myeloid Leukemia: Blasts are the predominant population and have a high nuclear to cytoplasmic ratio and generally lack granules. (Photo courtesy of Professor Peter G. Maslak, MD)

Cord Blood and Matched Related Donor Transplantation Compared in Acute Myeloid Leukemia

The prognosis of primary refractory and relapsed acute myeloid leukemia is poor, with a five-year overall survival of less than 10%. Allogeneic hematopoietic stem cell transplantation (HSCT) is the only... Read more


view channel

Global Immunofluorescence Assay (IFA) Market to Surpass USD 4 Billion by 2028 Due to Growing Burden of Infectious Diseases

The global immunofluorescence assay (IFA) market is expected to reach USD 4.01 billion by 2028, driven by the increasing global healthcare burden of chronic and infectious diseases, rising application... Read more
Copyright © 2000-2022 Globetech Media. All rights reserved.