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Publications

Our growing list of publications in peer-reviewed journals

Advancing DNA Sequence Technology 2016-12-03T06:23:59+00:00

Advancing DNA Sequence Technology

Extending Reference Assembly Models

Deanna M. Church, et al.
Genome Biology , 24 JAN 2015

The human genome reference assembly is crucial for aligning and analyzing sequence data, and for genome annotation, among other roles. However, the models and analysis assumptions that underlie the current assembly need revising to fully represent human sequence diversity. Improved analysis tools and updated data reporting formats are also required.

Automated sequence reading and analysis

West, J.
Nucleic Acids Research. Vol 16, Issue 5, Pp. 1847-1856 March 11, 1988

Our involvement with the development of today’s most advanced DNA sequencing technologies is extensive, built on years of work in the field.  This paper describes an early system development led by Personalis’ CEO, over 25 years ago.  Others members of our team have similarly deep technological experience.

Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays

Morgan AA, Chen R, Butte AJ.
J Am Med Inform Assoc. 2012 Jun 1;19(e1):e21-e27.

Next generation DNA sequencing is an alternative to array-based genotyping (which preceded it technologically).  Genotyping is less expensive per sample, but less comprehensive.  We have published on the comparison of these technologies for clinical applications specifically.

Detecting and annotating genetic variations using the HugeSeq pipeline.

Hugo YK Lam, Cuiping Pan, Michael J Clark, Phil Lacroute, Rui Chen, Rajini Haraksingh, Maeve O’Huallachain, Mark B Gerstein, Jeffrey M Kidd, Carlos D BustmanteMichael Snyder.
Nature Biotechnology 30, 226-229 (2012) 2012 | doi:10.1038/nbt.2134 Published online 07 March 2012

The DNA sequencing field benefited tremendously from the development of diverse algorithmic approaches at numerous laboratories.  Combining these algorithms into a comprehensive pipeline was a challenge taken on by a number of Personalis founders and employees, initially at Stanford.  Their work was particularly comprehensive in the areas of structural variation and implementation on highly parallel scientific computing systems, and led to the original version of the widely-adopted HugeSeq pipeline.  Personalis has continued this work and now offers a more advanced version of the pipeline to its customers.

Accurate whole human genome sequencing using reversible terminator chemistry

Bentley, D.R. et al (incl. West, J.S.)
Nature, Vol 456, 6 Nov 2008, p 53-59.

Personalis’ CEO was also previously CEO of Solexa and subsequently responsible for the DNA sequencing business at Illumina.  This article was the first publication of the Solexa / Illumina technology and several Personalis employees played seminal roles in the development of this technology. Whilst Personalis is open to the use of any DNA sequencing technology(ies), such close involvement in the development of this technology provides insight into the strengths and weaknesses of each available technology, and how best to optimize their use.