Tag Archives: Whole 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.

 

Revealed WGS of Oil Accumulating Diatom

bio-fuelMicroalgae are promising sources for biofuel production through the generation of carbon-neutral sustainable energy.

Biofuel from microalgae receives attention because it reduces CO2 emissions and does not use resources required for food production. A Japanese team revealed the whole genome sequence (WGS) of a marine diatom, Fistulifera solaris JPCC DA0580, which had been screened from their culture collection of microalgae (Tanaka et al., Plant Cell, 2015) as highly capable of oil accumulation. They said de novo assembly of this genome is so tough because it is alloploid, which means it has a very complex genome structure.

Finally, they could annotate about 20,000 genes on 42 chromosome pairs. They also identified a lot of genes which concern oil synthesis and, furthermore, they also analyzed activation patterns of these target genes.

I am sure this study will be a model case to highlight how NGS technologies can accelerate bioengineering!

Whole Genome Sequences Of World’s Oldest Living People Published

senior-asian-woman-100226669Researchers looked at the genome of some of the oldest living people. While they did not find a significant association with extreme longevity, the researchers published their genome findings. At least the data will be available as a resource for future researchers looking at the “genetic basis” of longevity.

There are 74 supercentenarians (110 years or older) alive worldwide, with 22 living in the United States. The authors of this study performed whole genome sequencing on 17 of them to explore the genetic basis underlying extreme human longevity.

“We were looking for a really simple explanation in a single gene,” said Stuart K. Kim, a Stanford geneticist and molecular biologist. “And we know now that it’s a lot more complicated, and it will take a lot more experiments and a lot more data from the genes of more supercentenarians to find out just what might account for their ages.”

From the limited sample size the researchers were not able to find protein-altering variants associated with extreme longevity, according to a study in PLOS ONE by Hinco Gierman from Stanford University and colleagues published November 12, 2014 . But they did find one supercentarian had a genetic variant related to a heart condition that had very little effect on his health considering he reached such and elderly age. The researchers noted that it is recommended by the American College of Medical Genetics and Genomics to report this instance as an incidental finding.

The whole genome sequences of all 17 supercentenarians are now available as a public resource so that they can be used to assist the discovery of the genetic basis of extreme longevity in future studies.

 

Compare to Large genome sequencing studies in the USA (posted August 26, 2014 )

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?).

Note: NGS in Diagnostic Testing

Yes, this amazing technology is not just a tool for basic researcher anymore, but has made its way in to the clinical routine testing. It currently all about exome sequencing and targeted gene panel analysis, but whole genome sequencing is expected to come into clinical routine soon. Have a read through this comprehensive article which describes very nicely which applications are suitable for the diagnostic testing and which may come in the future.

Read the article about NGS in diagnostic testing

Exome Sequencing At A Glance

Selective characterisation of the genome’s complete coding region

In humans, only 1-2 % of the genome is protein coding, the so-called exome. Exome sequencing is favoured over whole genome sequencing due to costs, efficiency and the easier interpretability of a much lower data volume compared to whole genome sequencing. It gains more and more clinical relevance in the determination of rare diseases as well as for cancer research and diagnostics. Furthermore, it’s a very important screening tool for genetic variations e. g. involved in mental disorders such as schizophrenia and is therefore increasingly used as one genomic application in drug discovery. Exome analyses are frequently conducted as trio analyses with one patient plus healthy parents, who serve as controls to filter out benign variants. They are not only performed on behalf of companies or academic research organisations, but also gain more importance in diagnostic applications for individuals.

The most common technologies for exome analysis are based on in-solution hybridisation. They use a protocol that first generates a whole genome library, and then enriches the exome portion of the genome. The well-established kits for this kind of analysis are from NimbleGen, Agilent and Illumina. The exome enriched DNA is then primarily sequenced with Next Generation Sequencing systems from Ilumina, like Illumina HiSeq. This approach is typically selected for projects with large sample numbers. One limitation is the incomplete coverage for some genetic loci. More consistent sequence coverage can be achieved by using a PCR based exome capture approach offered by Ion Torrent. This approach allows a very fast and a more uniform exome analysis ideal for small to mid-size sample numbers.

exome_sequencing

Whole Genome Sequencing And You

What is a genome? What are the basics of how whole genome sequencing works? What are the potential benefits and risks? Or do you just want to learn a bit more about this technology?
Ths video was developed by researchers at Mount Sinai’s Department of Genetics and Genomic Sciences and Department of Emergency Medicine with funding from the Charles Bronfman Institute for Personalized Medicine.

Just take a cool drink and relax while watching the video.

Whose Genome Has Been Sequenced? Hevea brasiliensis

de-novo-sequencingAll of us have at least once been doing experiments in the lab. And so everyone was confronted with latex gloves. And more and more of us developed a kind of latex allergy.

According to Rahman et al. “these allergies are triggered by certain proteins present in Hevea-derived natural rubber (NR). […] Hevea brasiliensis (Willd.) Muell.-Arg., also known as Pará rubber tree, is the primary commercial source for natural rubber (NR) production” (in total nearly 11 million tons in 2011 for all 2,500 rubber tree species).

Although rubber is used for > 50.000 products worldwide this is the first de novo sequencing approach. So far only transcriptome analysis studies were performed, which lack the non-coding regions of the genome.

What was sequenced?

Young leaves of Hevea brasiliensis RRIM 600. Genome size: ~ 2.15 Gb; 18 chromosomes

De novo sequencing strategy:

  1. Libraries: shotgun and mate-pair libraries (insert size: 500 bp) on HiSeq 2000; LPE libraries (insert sizes: 8 kb and 20 kb) on Roche GS FLX; Paired-end library (insert size: 2 kb) on SOLiD
  2. Coverage of all sequencing strategies together: ~ 43x (after filtering repeat-matching reads: ~ 13x = 27.86Gb)
  3. Data output: 143 scaffolds (total 1.119 Mb with N50 = 2.972 bp)
  4. Bioinformatics: CLC Workbench & Newbler assembler using different input data and different assembling strategies

Transcriptome sequencing strategy:

  1. Libraries: cDNA libraries
  2. Sequencing with Illumina HiSeq and Roche/454
  3. Bioinformatics: CLC Workbench assembler for the Illumina reads and Newbler for combining Roche and Illumina reads.

This de novo genome sequencing approach revealed that ~ 78% of the genome are repetitive regions. This study helps to improve breeding of H. brasiliensis by allowing marker assisted selection to further increase the disease resistance and minimize the allergenicity.

Read the complete publication here.

Whose Genome Has Been Sequenced? – Recent posts:

 

 

Whose Genome Has Been Sequenced? Latimera Chalumnae

de-novo-sequencingThe third de novo sequenced genome in our series Whose genome has been sequenced? is the “living fossil” Latimera chalumnae.

The most difficult part for this de novo genome sequencing approach was to get enough starting material. The authors even reported that their first approach was to use the Sanger technology, but is simply was not enough DNA available. Therefore they had to wait until the next generation sequencing techniques were stable enough to risk the sequencing (BioTechniques). Here are the sequencing facts of this study (Amemiya et al.):

What was sequenced?

A blood sample from an adult African coelacanth

De novo sequencing strategy:

  1. Libraries: shotgun library 61-fold coverage; 3 kb jumping library – 88-fold coverage, 40 kb fosmid library 1-fold coverage
  2. Illumina HiSeq 2000 (paired-end module)
  3. De novo genome assembly using the software ALLPATHS-LG
  4. RNA sequencing

RNA-Seq sequencing strategy:

  1. 4 cDNA libraries (1x mRNA-Seq library, 3x strand specific dUTP libraries from brain, gonad/kidney, gut/liver tissue) were sequenced using a HiSeq
  2. Data output: mRNA-Seq library ~ 210M paired-end reads;  dUTP libarires ~ 3-4 Gb of sequence/tissue
  3. Assembly was performed using Trinity

The genome sequencing helped to understand the possibility of this prehistoric fish to thrive on dry land and the phenotype that is so similar to 300 million year old fossils (BioTechniques).

Read the complete publication here.

Earlier published genomes:

Goat Genome Sequenced Using Whole Genome Mapping

Domestication of goats happened already thousands of years ago. Nowadays they are also used as models for biomedical research. However, one thing was still missing: a reference genome. Researchers from China could now close this gap by successfully sequencing the genome of a domestic goat.

To reveal the secrets of the goat genome the researchers applied a hybrid approach of Illumina shotgun sequencing and whole genome mapping (WGM) using the Argus system from Opgen. As a result, the number of scaffolds could be reduced from 2,090 to 315. This demonstrates that whole-genome mapping for large genomes can be a replacement for traditional genetic maps for de novo assembly (Dong et. al).

This reference genome can now be used for mapping reads of other goats to identify SNPs and other variants that could play a role for breeding, cashmere fiber prodcution or different goat behaviours (Dong et. al).

If you are interested in more information about optical mapping, read our dedicated blog posts: What is optical mapping? and Creating the perfect genome assembly.