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Genetic Linkage

Sequencing the Genomes of Dead People

Last Wednesday, at “Career Night” during the American Society of Human Genetics annual conference in Baltimore, I was stationed next to Robert Steiner, MD, from the Marshfield Clinic Research Foundation in Wisconsin. With young scientists circling us like electrons around nuclei, I never got the chance to break away to talk to him. But I did overhear him discussing the Genomic Postmortem Research Project, an effort to sequence the genomes of 300 dead people.

I was fascinated.

Would knowing the information encoded in the DNA of the deceased have changed their health care? I went to the talk on the project the next day to find out about this clever test of the value of genome sequencing.

A BRIEF HISTORY OF HUMAN GENOME SEQUENCING
Genomes transcend time. The beauty of seeking clues to health in DNA sequences is that this relatively immutable record is present in nearly every cell of an individual. Two copies of our genomes are nestled into the nuclei of cells of our kidneys and spleens, bone marrow and eyeballs, the same blueprint stamped over and over down the cell lineages at every mitosis, with a few somatic mutations spewed here and there. The genome in the fertilized ovum matches that in the cells of the 90-year-old it might someday become, given good genes and a lot of luck. And DNA rests within the bone cells of the skeleton long after death, the mitochondrial satellite source even more resistant to time and trauma.

"The" human genome was first sequenced in 2001 or 2003, depending upon which draft is cited, and included a compendium of DNA donors from the International Consortium and lone genome of J. Craig Venter from the Celera Genomics version. The genome sequence of another rock star of science, James Watson, was next. Then came a few “firsts,” such as the genome of a man called simply "YH," a Han Chinese. Representatives of other population groups followed.

Then came the famous. The late Steve Jobs and Christopher Hitchens were sequenced in futile attempts to combat their cancers. Henry Louis Gates Jr. did it to trace his African roots. The actress Glenn Close and musician Ozzy Osbourne reportedly did it to better understand mental illness in their families.

With genome sequencing costs plummeting from an initial $22 million to hovering around $1,000, it’s no longer restricted to the ultra wealthy, and in fact possibly five million human genomes will be sequenced by 2020. The Precision Medicine Initiative Cohort Program, which I blogged about two weeks ago, will contribute one million of them.

Meanwhile, genome (and exome, the protein-encoding part) sequencing is being used increasingly to end multi-year diagnostic odysseys, as I wrote about here, in JAMA, and in Medscape, which link to the centers doing the work. Knowing a sick child’s genome sequence can explain past symptoms while guiding future care and treatment choices. And it isn’t just sick kids. Human genomes are being sequenced from gametes to embryos to supercentenarians, the oldest old.

Genome sequencing extending back in time isn’t new, just on a different scale from the postmortem project’s 300 samples. The publication list of Svante Pääbo, Director of the Max Planck Institute for Evolutionary Anthropology, reveals these efforts. Since 1980, he’s probed the bones, hair, spit, and excrement of many species, analyzing the genomes of Denisovans, Neanderthals, a person who lived in what's now Romania 40,000 years ago who had Neanderthal forebears a mere four to six generations back, Egyptian mummies, and Ötzi the ice man. The first ancient African genome – from circa 4,500 years ago in Ethiopia – was reported just a few weeks ago, from Ron Pinhas at University College Dublin and Marcos Gallego Llorente from the University of Cambridge. Analysis of ancient DNA has revealed the ills of past peoples, from infections and injuries to inherited diseases.

DNA from the more recent past has been scrutinized too, including posthumous diagnosis of Rett syndrome from a baby tooth and “rescue karyotyping" to reconstruct genetic clues to pregnancy losses.

300 DEAD GENOMES
The Genomic Postmortem Research Project is being led by Murray Brilliant, Ph.D., with Simon Lin, M.D. and Min He, Ph.D., and funding is from Complete Genomics. The goal: “to sequence the entire genome in 300 patients with long-term electronic medical records at Marshfield Clinic to determine (after the fact) if genomic knowledge could have positively influenced their medical care.”

It’s hard to know what, exactly, to look for among all those genomes, especially because we don’t know what all the 20,000 or so genes and their many variants do. But the Marshfield Clinic’s website and newsletters offer a compelling list to start:

• Chronic diseases (age-related macular degeneration, heart attack, type 2 diabetes, cataracts, and glaucoma)
• Cancers of the prostate, breast, and lung
• Susceptibility to bacterial infections and flu
• Fragile X syndrome premutation prevalence
• Iron metabolism
• Pharmacogenetics of metformin, statins, proton pump inhibitors

The researchers are sorting through 27+ million gene variants from the corpses, seeking those that could be used for disease prevention, detection, and personalized treatment and monitoring. Dr. He listed their resources:

SeqHBase, a “big data toolset” that distinguishes de novo (new) mutations from inherited ones, and whether the variants are present in one copy (a heterozygote) or two copies (a homozygote or a compound heterozygote).
ClinVar looks for disease or drug-associated gene variants.
• The ACMG (American College of American Genetics and Genomics) lists 56 mutations associated with 24 conditions, known simply as “the 56,” that it recommends be reported to patients if they show up as secondary findings, because they are “actionable.”
• NHGRI lists 112 actionable incidental findings from its exome sequencing project, which includes 52 of the ACMG 56.

The most daunting challenge right now is to classify gene variants – we can't call them all mutations anymore due to negative connotations – as to how harmful evidence indicates they are. To make a very long story short, variants are classified as pathogenic, likely pathogenic, the dreaded “variant of uncertain significance,” likely benign, and benign. As the number of sequenced genomes climbs, the proportions will shift, with the numbers of VUS and the use of the word “likely” declining as pathogenic and benign designations rise. Uncertainty will certainly fade. Dr. He raced through some preliminary data that indicated a disturbing number of “variants of uncertain significance.” Then he described two interesting cases.

#1 A woman died from breast and ovarian cancer at age 59. She had no family history of cancer, and had never had a mammogram. Yet her genome sequencing revealed a rare pathogenic variant of BRCA1. “If the gene variant had been detected prior to her diagnoses, at an early age, it is possible that the cancers could have been predicted and/or prevented,” Dr. He said.

Hereditary hemorrhagic telangiectasia#2 A patient with deep vein thrombosis, a vascularized kidney cancer that had spread to the brain and lungs, and arteriovenous malformations (tangles of abnormally connected blood vessels), had hereditary hemorrhagic telangiectasia type 1 – a disorder of the vasculature. The diagnosis explained the symptoms, and would have suggested drug treatments old (such as thalidomide) and new (such as the anti-VEGF drug bevacizumab (Avastin).

Pharmacogenetic findings were intriguing – 281 of the 300 deceased individuals had meaningful variants among the 30 genes that the FDA recognizes as influencing the metabolism of more than 100 drugs. Examples include variants of CYP2C9 and VKORC1 and warfarin dose; DPYD and TPMT and the cancer drugs 6-mercaptopurine and irinotecan; CYP2D6 and tamoxifen and codeine; and a frighteningly long list of anti-depressants and anti-psychotics that are under or over active depending upon genotype. Several individuals had variants of SLC01B1 that increase risk of developing myopathy with use of the cholesterol-lowering drug simvastatin (Zocor).

If my grandpa would have had crippling muscle pain from Zocor and my doc was now trying to foist it on me, I’d want to know. But because the Genomic Postmortem Research Project is what it says – research – a protocol for contacting descendants who might want to know relevant genetic risk information about drugs and disease susceptibilities isn’t in place. The bioethicists will have to figure out informed consent from corpses.

Meanwhile, it seems pretty clear that when newborn genome sequencing becomes routine, DNA information may be the greatest gift from generations past.

Next week I will be moderating a session on Precision Medicine at the National Organization for Rare Disorders Summit in Washington, DC. I’ll be sure to eavesdrop again!



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