Tuesday, 26 June 2012

Exome sequencing as potential diagnostic tool in Charcot-Marie-Tooth

Exome sequencing has proved itself as a valuable tools for rapid molecular diagnosis, particularly when a disease can be caused by several mutations in different genes. Here is a good example of applying WES to discover new mutations in CMT patients with no mutations in the main disease associated loci.

Byung-Ok Choi, Soo Kyung Koo, Mi-Hyun Park, Hwanseok Rhee, Song-Ju Yang, Kyoung-Gyu Choi, Sung-Chul Jung, Han Su Kim, Young Se Hyun, Khriezhanuo Nakhro, Hye Jin Lee, Hae-Mi Woo, Ki Wha Chung.

Charcot-Marie-Tooth disease (CMT) is one of the most common inherited neuropathies and is a genetically and clinically heterogeneous disorder with variable inheritance modes. Since several molecules have been reported to have therapeutic effects on CMT, depending on the underlying genetic causes, exact genetic diagnostics have become very important for executing personalized therapy. Whole-exome sequencing has recently been introduced as an available method to identify rare or novel genetic defects from genetic disorders. Particularly, CMT is a model disease to apply exome sequencing, since more than 50 genes (loci) are involved in its development with weak genotype-phenotype correlation. This study performed the exome sequencing in twenty five unrelated CMT patients who revealed neither 17p12 duplication/deletion nor several major CMT genes. This study identified eight causative heterozygous mutations (32%). This detection rate seems rather high, since each sample was tested before the study for major genetic causes. Therefore, this study suggests that the exome sequencing can be a highly exact, rapid, and economical molecular diagnostic tool for CMT patients who are tested for major genetic causes.

Thursday, 21 June 2012

NGS as diagnostic tool: "FDA discusses issues with regulating NGS disease tests"

NGS is a powerful tool for the discover of new disease genes. The evidences of its potential succesful application in the diagnostic field grows day by day, as well as grows the pressures of scientific and medical community on those institutions that have the role to decide on these issues. Recently the road to this goal seems to be even more short. Here we report the link to a post on GenomeWeb describing how the FDA is seriously considering the potential of NGS technology as a future diagnostic tool.

Image credit:

Wednesday, 20 June 2012

NGS PubMed Highlights

Here we go with a new category of posts on the NGS blog: NGS PubMed Highlights. Whenever we want to draw attention to an interesting paper with no further comments, we will create a "PubMed Highlights" post with the PubMed citation, abstract as well as a link to the entry.

NGS PubMed highlights: Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA

Sci Transl Med. 2012 May 30;4(136):136ra68.

Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA.


Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.


Plasma of cancer patients contains cell-free tumor DNA that carries information on tumor mutations and tumor burden. Individual mutations have been probed using allele-specific assays, but sequencing of entire genes to detect cancer mutations in circulating DNA has not been demonstrated. We developed a method for tagged-amplicon deep sequencing (TAm-Seq) and screened 5995 genomic bases for low-frequency mutations. Using this method, we identified cancer mutations present in circulating DNA at allele frequencies as low as 2%, with sensitivity and specificity of >97%. We identified mutations throughout the tumor suppressor gene TP53 in circulating DNA from 46 plasma samples of advanced ovarian cancer patients. We demonstrated use of TAm-Seq to noninvasively identify the origin of metastatic relapse in a patient with multiple primary tumors. In another case, we identified in plasma an EGFR mutation not found in an initial ovarian biopsy. We further used TAm-Seq to monitor tumor dynamics, and tracked 10 concomitant mutations in plasma of a metastatic breast cancer patient over 16 months. This low-cost, high-throughput method could facilitate analysis of circulating DNA as a noninvasive "liquid biopsy" for personalized cancer genomics.

[PubMed - in process]

A whole human genome in less than two weeks through a sequencing service

Illumina today launched RapidTrack WGS, a whole genome sequencing service that delivers a whole human genome in less than two weeks. This is fastest sample-to-data turnaround time of any whole human genome sequencing service available today.
From the Illumina press release: "RapidTrack WGS utilizes Illumina's new HiSeq 2500 sequencing system, which is capable of sequencing a complete human genome in one day. In combination with an accelerated sample preparation protocol and the Company's new iSAAC genome alignment software, sample-to-data cycle time for a complete human genome is five days with the new service. To allow for queue time, RapidTrack WGS guarantees a turnaround of less than 14 days".

Tuesday, 19 June 2012

1,000 rare diseases in the aim of BGI@CHOP

The large collaboration between BGI and Children's Hospital of Philapdelphia (CHOP) for the study of pediatric diseases has now been expanded to include the study of 1,000 rare diseases with a single-gene inheritance pattern. This initiative is based on the well established collaboration between BGI and CHOP, started this fall, and on the consideration that rare diseases individually affect a small percentage of the population but taken cumulatively they affect roughly one in every 12 newborn children.

Combining the sequencing and bioinformatic skills of BGI with the biobank and data from CHOP the team hopes to rapidly identify variants that could be used for the diagnosis of these rare diseases and and the development of new therapeutical interventions.

Both institutions gave the official announcement yesterday (18th June).
(BGI here and CHOP here).

Monday, 11 June 2012

Noninvasive Whole-Genome Sequencing of a Human Fetus

This is the title of a manuscript published on June 6 on Science Translational Medicine.
For the first time researchers have decoded the entire genome of a 18 weeks fetus using only a blood sample from the mother and a saliva sample from the father.
Scientists have long known that a pregnant woman's blood plasma a few weeks after conception contains cell-free DNA from her developing fetus a few weeks after conception. About 10 percent of the cell-free DNA in a pregnant woman's blood plasma comes from her fetus although the concentration varies among individuals.
Comparing the woman's plasma DNA with genome sequences obtained from the father's saliva and the mother's blood allowed the researchers to identify fetal DNA sequences that they could computationally piece together into the child's genome.
To identify the fetal DNA, Shendure and colleagues first used a new technique to identify haplotypes that could be traced back to the mother’s genome. This information, along with data from the father’s DNA sample, allowed the researchers to determine which parts of the maternal and paternal genomes were inherited by the fetus.
Comparison with the baby's genome sequence determined after birth showed the team's predictions to be more than 98% accurate.
The scientists also successfully repeated the experiment on a second younger fetus at a time (8.2 weeks after conception) when less fetal DNA is in the mother's blood.

(Image credit: Shedure Lab)

Wednesday, 6 June 2012

Hepatocellular carcinoma on GigaDB: another avalanche of free data for the scientific community

The Asian Cancer Research Group has released on GigaDB the raw data from its project on Hepatocellular Carcinoma. This is a really huge dataset including 30X whole genome sequences from both health and tumor tissues obtained from 88 asian patients. And if it may be not enough to satisfy your data-analysis desires, raw data from gene expression analysis on these samples are also available deposited in the GEO database.
From the project's web site: "Genomic DNA was purified for at least 30-fold coverage paired-end (PE) sequencing, and PE reads were mapped on human reference genome (UCSC build hg19) and HBV (NC_003977). Two sequencing libraries with different insert size were constructed for each genomic DNA sample (200bp and 800bp). Paired end, 90bp read length sequencing was performed in the HiSeq 2000 sequencer according to the manufacturer’s instructions. Raw gene expression profiling data of these human HCC samples have been deposited to GEO with the accession number GSE25097."
The study has been recently described in a letter to Nature Genetics (Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma).