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Different QM/QA Levels for Genomics Analyses

quality1High quality standards are essential for non-clinical QC testing. When we obtained GLP certification, people ask me about relevant QM/QA levels for genomics analyses. This is what I tell them:

ISO 9001 – the basis

The ISO 9001 standard is a global quality management standard that favours process orientation, customer orientation, satisfaction and continuous improvement. ISO 9001 provides the basis for a quality management system ensuring that all processes are documented and defined in SOPs. In an ISO 9001 compliant laboratory responsibilities are clearly defined, all work environment and infrastructure is suited for its intended purpose. Equipment and facilities are qualified and maintained and measuring and testing equipment requires regular calibration. Also the staff is qualified and well trained and the training is recorded. Supplier management and purchase are controlled processes. Non-conforming work and failures are corrected and documented. Processes for corrective and preventive actions are implemented, as well as a proper complaint management. In an ISO 9001 QM system all business processes are monitored (e.g. by internal and external audits). Customer feedback and all data obtained are analysed on a regular basis. These data and information are the basis for continuous improvement of the ISO 9001 QM system.

ISO 17025 – assures technical valid results

The ISO 17025 is derived from ISO 9001. With an ISO 17025 accreditation a laboratory demonstrates its technical competence and the ability to generate technical valid and correct results. In addition to the ISO 9001 standard the participation in external proficiency testings is mandatory. Furthermore, the documentation of the lab procedures is a lot more detailed and involves dedicated protocolling procedures.

GLP – the gold standard to conduct non-clinical safety studies

The GLP (Good Laboratory Practice) standard adds on top of that a framework in which laboratories non-clinical safety studies are planned, performed, monitored, recorded, reported and archived. GLP helps to assure regulatory authorities that submitted data are a true reflection of the results, obtained during the study and can therefore be relied upon when making risk/safety assessments. In addition to the requirements of ISO 9001 and ISO 17025, GLP involves the nomination of a study director and dedicated trained personnel for GLP compliant processes. A study will involve always the creation of a study plan which will be signed by the study director. All processes applied in the study need to be described within the study plan. Any deviations to the study plan will lead to an amendment of the study plan. After completion of the analyses the study director generates a final report signed by Study Director and QA/QM. It also includes a signed QA-and GLP compliance statement. Each study is audited by quality assurance staff. Furthermore, there needs to be restricted laboratory access and restricted access to relevant data as well as dedicated archiving procedures (GLP archive) for all GLP documents and raw data..

GCP – similar to GLP with focus on clinical studies and patient safety

The GCP (Good Clinical Practice) standard is very similar to the GLP standard; however it is relevant only for clinical studies and has thus a focus on patient safety and reporting of adverse drug events. In a study that involves GCP compliance it has to be assured that only such things are analyzed that a study patient has consented to.

Feel free to write a comment for further clarification. I am looking forward to get in contact with you.

Cheers, Katrin

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.

A major upgrade of SAMTools: CRAM format to reduce NGS data load

SAMTools, one of the most popular NGS sequence analysis tools has recently been upgraded by Computer scientists at the Wellcome Trust Sanger Institute. SAMTools is a set of utilities which allow the manipulation of alignments in the SAM/BAM format. SAM is the acronym for Sequence Alignment/Map format, whereas BAM is just the binary form of SAM. SAM can be seen as the worldwide standard for storing large nucleotide sequence alignments.

SAMTools 1.0, the revised version of the free program suite now allows researchers an improved handling of their sequencing data. Further to the existing SAM and BAM file formats, SAMTools now supports the new CRAM format. Basically, CRAM files are alignment files, just like BAM files – except that their size is reduced by 10 -30%. For better handling even greater compression – up to 100-fold – can be achieved in the “lossy” mode, that still preserves the most important information. The savings in storage that CRAM offers could be achieved by incorporating data compression techniques which were cooperatively developed by the Sanger Institute and the EMBL-European Bioinformatics Institute.

“This major rebuild of SAMTools reflects our commitment to supporting the global use of sequencing data,” says Dr Richard Durbin, Head of Computational Genomics at the Sanger Institute. “Genome science worldwide relies on fast and efficient data analysis and storage, and SAMTools 1.0 fulfills this need by supporting new sequencing and analysis technologies”. Dr. John Marshall from the Sanger Institute is highly optimistic that the widespread uptake of the new format will lead to lower data storage costs on a global scale (complete article).

I am curious on how the new format is going to be adapted by the genomic community. By the way did you know that SAMTools has been downloaded more than 225,000 times?

Large genome sequencing studies in the USA

senior-asian-woman-100226669The launch of the Illumina HiSeq X Ten enabled them to put in practice their plans and great visions. I’m speaking of two persons of great influence in the United States. This year, Dr. J. Craig Venter, known for being one of the first to sequence the human genome and Patrick Soon-Shiong, considered as the world’s richest doctor, both revealed some details about their large scale sequencing projects:

  • J. Craig Venter founded the company Human Longevity that aims to develop treatments for cancer and age-related conditions. To unveil the mechanisms how people can live long and healthy lifes, the company will become one of the largest DNA sequencing facilities in the world. The plan is to set up a sequencing center that is capable of sequencing 40,000 human genomes a year.
  • Patrick Soon-Shiong recently announced that his company NantHealth is purchasing sequencers being able to sequence 22,000 genomes annually. The samples will derive from the 22,000 patients diagnosed with cancer annually at the 34 hospitals owned by Providence Health & Services. Consequently, the company from Soon-Shiong probably will become the first one using their sequencing capacity for clinical sequencing on a large scale.

Such huge collections of sequencing data make it possible to uncover the molecular causes of an complex process as aging or such a diverse and complex disease as cancer in a general approach. Big and very valuable databases will be created, that may contribute to develop new pharmaceuticals or develop personalized therapies.

The future of miRNA analysis

We asked you in which technology you see the future of miRNA analysis.
Find here the voting of the 102 participants:

miRNA

 

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

Why is Illumina so successful? Watch an interview with Illuminas CEO

In the 2nd quarter of 2014 Illumina reported adjusted earnings of 57% per share – most probably the biggest increase in the companies history. Watch this interview with the CEO of Illumina, Jay Flateley, to learn more about the reasons of Illumina’s success.