Tag Archives: Genome sequencing

Rapid Genome Sequencing in NICUs and PICUs

protocolSTAT-Seq to rapidly detect thousands of genetic diseases.

A recently published study in The Lancet Respiratory Medicine reveals the early results of the clinical usefulness of rapid whole genome sequencing in neonatal and pediatric intensive care units (NICUs and PICUs). Children’s Mercy Kansas City’s STAT-Seq test helped diagnose a genetic disease in more than one half of 35 critically ill infants tested, compared to just 9% with standard genetic tests.

Besides the medical impact on treatment strategies I want to share some information about STAT-Seq.

STAT-Seq, which runs on Illumina’s HiSeq 2500, is first of all a research protocol. It is the fastest whole genome test that might take less than 50 hours from test order to delivery of an initial report once it is fully implemented in the lab. STAT-Seq can identify mutations across the genome associated with approximately 5,300 known genetic diseases.

The study showed a significantly improved diagnosis rate for whole genome sequencing versus traditional testing. But it did not show an improvement over what is typically seen in exome sequencing. The latter only examines the parts of DNA that code for proteins, the body’s basic building blocks.

Right now exome sequencing is the more commonly used diagnostic tool because the technology is cheaper and more readily available. Cost effectiveness was not examined in the study, but the costs of genome sequencing are falling rapidly. Currently, the best available cost runs around €3,500 ($4,000), but many genomic researchers say it could drop down to €1,500 ($1,700) until the end of this year.

Whole genome testing could become a more useful tool than exome sequencing in the long run because it provides more complete information. Genes account for less than 25% of the DNA in the genome. The remainder includes areas that control how genes are turned on and off as well as “junk” DNA whose function isn’t fully understood.

Get other aspects of the study in GenomeWeb.

 

Whole genome sequencing a complete island

http://commons.wikimedia.org/wiki/File:Coat_of_arms_of_Iceland.svg

http://commons.wikimedia.org/wiki/File:Coat_of_arms_of_Iceland.svg

Two days ago a groundbreaking study was published in Nature Genetics: Whole genome sequencing of 2,636 Icelanders and Genotyping of 104,220 Icelanders.

The advantage of using a small population like the Icelanders for this kind of study is that there are fewer rare variants, but sometimes also a higher occurance of some of these variants.

For the study, geenomic DNA was isolated from white blood cells and subsequent sequencing was performed on GAIIx and HiSeq instruments. The resulting reads were aligned to the human reference genome (NCBI Build 36 (hg18).

Gudbjartsson et al. then examined the data from different angles. For example, they looked for geographical dependencies for specific variants or how the data can be used to learn more about phenotypes and their underlying genomic pattern. But they also report an example “how rare variants […] can be used to analyze clinical problems”. (Gudbjartsson et. al)

Since every human being has a unique genomic pattern I think studies like this are of high importance to learn more about disease related genotypes. This will help to gain confidence in the results that we get from molecular diagnostic assays for disease treatment now and in the future.

Read the complete publication here.

How to handle variants in a reference genome

When talking about genome sequencing the human genome project is one of the best known projects. “Building” a reference genome that helps to identify disease-causing mutations is only one of many goals for the human reference genome.

But I am sure that all of you already asked the question: how can a reference genome even exists? On earth we have more than 7 billion people and among that many different characteristics. So how can one human reference serve for all mankind?

The Global Alliance, lead by David Haussler, recently won a $1 million grant to create a graphical model of the human genome (BioTechniques). The graph model should help to visualise variants as alternate pathways. Like that a more comprehensive picture of “naturally occuring variants” and disease causing variants might be gained. To support this approach, they got access to 300 complete human genome sequences from the Broad Institute in Cambridge.

From my point of view this is a great idea and I hope it helps to further pave the way how the massive amounts of sequencing data can be handled and interpreted in the near future!

Read the complete article at BioTechniques.com

 

Prepare NGS for clinical use

Molecular diagnostics (MDx) is to my opinion the most sensitive application for all kinds of molecular biology techniques like PCR, Sanger Sequencing or Next Generation Sequencing. Today, NGS is still a niche application and needs further improvement to be a common tool for MDx. One thing that is lacking is the standardisation of NGS for clinical use.

The NGS Working Group, established by the Friends of Cancer Research worked out a master plan (The ASCO Post), with critical points that need to be addressed to use NGS more commonly:

1. Define a regulatory pathway for cancer panels (a selection of multimarker gene assays) intended to identify actionable oncogenic alterations (those with supporting data to create risk-benefit assessment of treatment choice) that allow flexibility in the appropriate FDA medical device pathway—for instance, one based on risk classification of different panel components depending on the specific marker.

2. Approaches to validation studies should be based on the types of alterations measured by the assay rather than on every alteration individually.

3. Determine the contents of a cancer panel by classifying potential markers based on current utility in clinical care and clinical trials and peer-reviewed publications, as well as recognized clinical guidelines. Draw upon various sources to determine the recommended marker set for an actionable cancer panel.

4. Promote standardization of cancer panels through development and use of a common set of samples to ensure reproducibility on each platform.

5. Establish a framework for determining an appropriate reference method rather than relying on any single method for all studies.

Get more information to each proposal here.

Whose genome has been sequenced? Brassica napus

de-novo-sequencingBrassicas napus, also known as oilseed rape, was formed more than 7000 years ago by allopolyploidy (chromosome doubling from to Brassicas species). Of course the genome mutated further and so it is known today that during this evolution some genes were preserved and further “improved” (e.g. oil biosynthesis genes), whereas others were lost over the course of time (e.g. glusoinolate genes).

Chalhoub et. al now sequenced the genome, because it can help to “provide insights into allopolyploid evolution and its relationship with crop domestication and improvement” (Chalhoub et. al).

What was sequenced?

Young fresh leaves from the Brassica napus French homzygous winter line “Darmor-bzh“.

Sequencing strategy: Whole genome sequencing

  1. Libraries & Sequencing:
    Roche GS FLX: ~ 70 Million reads, Average Read length: ~ 368 bp, Genome coverage: 21.2 %
    Sanger BAC Seq: 141k reads, Read length: 650 bp; Genome coverage: 0.1%
    Illumina HiSeq:  ~375 Million reads, Read length: 36, 76, 108 and 150 bp, Genome coverage: 53.9%
  2. Data output: 44.146 contigs and 20.702 scaffolds
  3. Results: A final assembly of 849.7 Mb (using SOAP and Newbler) with 89% nongapped sequences.

After genome assembly the genome was mapped to other species (e.g. B. rapa and B. oleracea) and this helped to find several interesting genes and gene variation that help to understand the complete evolution better.

Read the complete publication here.

Whose Genome Has Been Sequenced? – Recent posts:

Think Big: The UK 100,000 Genome Project

In late 2012 the 100,000 genome project was launched. UK Prime Minister David Cameron announced a new initiative led by the National Health Service to sequence the genomes of up to 100,000 people and to use their genomic information in treatment and studies of cancer and other diseases. The government set aside 100 million GBP for this project.

hiseq-x-tenGenomics England which is heading the project now named 10 firms that have been selected to for the assessment of the next phase of the project. The companies are Congenica; Diploid; NantOmics; Genomics Ltd.; Illumina; Qiagen; Lockheed Martin; NextCode Health; Omicia; and Personalis.

As part of the recently completed stage, Genomics England in February sent out a questionnaire to 28 participants in relation to 10 cancer/normal samples and 15 rare disease trio samples.

Illumina is partnering as well and will contribute with the ultra-high throughput sequencing platform HiSeq XTM Ten.

What will be the next step? Sequencing everyone?

Do you want to share your biggest secret?

people_09Should we all get our genome sequenced? And share the information? Just today I read two articles in GenomeWeb regarding human genome sequencing. With, to my opinion, opposite views regarding sharing information from human genomes.

The first article is about the 23andMe project: Here two different groups of people said, that with the functionality “check for close relatives” box they ended up in real crisis in their family. In one case the parents divorced since the close relative box showed that the husband had already a child with another women (prior this marriage). And in the other case a girl found out that she has a brother, whom her mother has giving up for adoption.

So for me this is a clear indicator that simply sharing the genome information might really cause more problems than it can solve.

Exactly the opposite is asked for by George Church. From his point of view for eradicating diseases, creating unlimited energy sources and so on a public access to as many genomes (human and non-human) as possible is a prerequisite.

And I think I could agree to that partially, if we talk about bacteria or plant genomes. But I think we are not ready for a wide sharing of human genome information.

What also became clear to me is that we are not a lot further, than 2 years ago (Genomics – A Curse Or A Blessing?).

Genome sequencing identified Jack the Ripper

It is very likely, that the murders from Jack the Ripper are by far the best-known crime series in the world. The London police had six key suspects for the murders and one of them now could be identified as the killer (MailOnline).

The piece of evidence that was used to identify the murderer was a shawl found be one of the victims, that contained DNA from the victim as well as from the suspect. Using a whole genome sequencing approach, Dr. Louhelainen and his group extracted the 126-year-old DNA and compared it with descendants of the suspect. Read the complete article at DailyMail Online.

Are you ready to have your genome sequenced?

Genome sequencingLast month we asked if you would be interested in sequencing your genome. If the costs would be lower, the majority said “YES”.

More than 20% answered that their genome has already been sequenced. Personally, I would be very interested to know what they did with the data output.

 

If you are one of the guys who voted “I already have” please submit a comment why you decided to have your genome sequenced.

Whose Genome Has Been Sequenced? Belgica antarctica

de-novo-sequencingExtreme conditions require extreme actions. And this is what the midge Belgica antarctica has done. The midge lives exclusively in the Antarctic and in order to survive shrinked its genome to the smallest possible size. As of today, this is the smallest insect genome that has been sequenced.

Kelley et. al. now sequenced the genome of Belgica antarctica with the aim to learn more about how insects in general can adapt to the most extreme conditions.

What was sequenced?

Two fourth instar larva (Belgica antarctica) collected near Palmer Station, Antarctica.

Sequencing strategy: Whole genome sequencing & RNA-sequencing

  1. Libraries & Sequencing: 1 channel 2x 100 bp Illumina HiSeq 2000 (SG library (400 bp insert)) and one SMRT-cell of a 10 kb fragment library on PacBio RSII (P4 DNA Polymerase)
  2. Data output: 92 M paired-end reads from the shotgun sequencing with Illumina. These resulted in 5,422 contigs. Using the paired-end RNA-Seq data the number of contigs has been reduced to 5,064. Genome coverage with Illumina sequencing ~ 100x.
  3. Results: The total genome is ~ 99 Mbp.

For the PacBio sequencing a second larvae was used. But due to the low input of genomic DNA the PacBio data yielded only in a modest improvement in assembly. This underlines the need of a long-read sequencing technology with low input DNA material.

The de novo sequencing of the midge Belgica antarctica revealed that the smalll genome size is achieved by a reduction in repeats, TEs and intron size.

Read the complete publication here.

Whose Genome Has Been Sequenced? – Recent posts: