This research began, like a lot of research does, with a conversation around an idea. Aravinda Chakravarti, PhD, (a prominent Johns Hopkins geneticist) discussed with Tim Harkins, PhD, of the Life Sciences Solutions Group within Thermo-Fisher Scientific how so much research is centered on the negative. A mutation interrupts the coding region of a gene which then causes a particular adverse health condition (Chakravarti studies the genetics of complex diseases like autism and hypertension).
But what about research centered on the positive? A situation where an individual’s genetic makeup works perfectly, enabling a healthy life far beyond an average lifespan?
A researcher in Amsterdam approached Harkins with the prospect of sequencing the whole genome of a supercentenarian. She was a woman who lived 115 years and had neurocognitive abilities better than many 65-year-olds, and who upon her death in 2005, was found to have a brain completely free of the beta-amyloid plaques that normally characterize an aging brain (abundant in Alzheimer’s). Harkins was initially doubtful of the value of a single individual, an N=1 experiment. What would a human genome sequence offer with only one sample?
It turns out that a single human genome sequence from a remarkably healthy 115-year old supercentenarian can offer a lot. But first a few observations about how the sequencing was done.
SOLiD™ Paired-End Sequencing (50 x 35 base pairs) with Exact Call Chemistry was performed on both occipital brain lobe and peripheral white blood cells to over 60x coverage. After stringent filtering (BioScope read mapping against hg19 and then use of variant callers SAMtools and GATK in parallel, with only calls from both tools being used), the overlapping SNVs and indels were confirmed using custom Ion AmpliSeq™ technology on an Ion PGM™ Sequencer with Ion 318™ chip, and those that failed to confirm due to long repetitive sequence or homopolymers were confirmed using capillary electrophoresis.
This is an example of the use of a high-throughput NGS platform like the SOLiD™/5500xl-W systems to get extremely accurate human genome sequence as a discovery tool, followed by use of the benchtop Ion PGM™ System and custom Ion AmpliSeq™ technology for validation of these variants, along with Sanger sequencing. The Ion Torrent™ business group within Thermo-Fisher Scientific supported this work by carrying out all of the sequencing in-house through our collaborations group.
The results, published recently in Genome Research, were telling. By comparing the ‘baseline’ genome of the occipital brain (where cell division ceases to occur around the age of four) to the genome of the circulating white blood cells (which replenish constantly from a pool of constantly replenishing hematopoeitic stem cells (HSCs) estimated to number from 10,000 to 20,000 per individual), the rate of somatic mutation could be calculated. But that depended upon the population of blood cells coming from a limited number of HSCs, or the minor allele frequencies of all the varied subpopulations would be below the detection limit.
The findings were striking. About 450 somatic mutations were detected, all non-deleterious mutations in A-T-rich regions, and remarkably, about 65% of the differentiated WBCs came from only two progenitor HSCs. By the researcher’s estimate, given a 115-year timeframe and the 25–50 week self-regeneration rate of HSCs, there are about four mutations that occur per year, or about three mutations per cell division.
Another intriguing aspect of this work is the length of the telomeres of the brain cells compared to the WBCs. The WBCs had telomeres 17-fold shorter—and telomere length is known to be a marker of aging.
Discussing this research with Harkins, Chakravarti mentioned how valuable it would have been to have sampled this individual’s WBCs over the course of decades to trace back the mutation rate with greater precision. These longitudinal studies are important, and take place over timeframes that are so long (and would require the enrollment of hundreds or even thousands of volunteers) that only an organization like the government can undertake them.
Sure enough, the National Institutes of Health has several longitudinal studies and there are a few accepting enrollments. For example, the New England Centenarian Study at Boston University is looking for individuals to enroll who are 105 years and older, along with their family members. At Albert Einstein University, the Longevity Genes project focuses on Ashkenazi Jews who have at least one parent who survived until at least age 95. The project is actively looking to enroll family members. There are also recent commercial enterprises such as Craig Venter’s recently founded Human Longevity Institute and Google’s new venture Calico, both aimed at extending human lifespan and both incorporating genomics into their plans.
References: “Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis”, May 2014, Genome Research 24(5):722-742, doi: 10.1101/gr.162131.113