Ricki Lewis

When it comes to estimating risk of a disease that is either genetic or has a genetic component, ancestry of an individual plays an important role. That's because increased risk of a particular health condition may be associated with a gene variant (aka mutation) in one population, but not another. Someone from a group not represented in the data on which a clinical test is based could receive an incorrect risk assessment, or even prescribed a drug unlikely to work.

A team from the Johns Hopkins Bloomberg School of Public Health and the National Cancer Institute has developed a new algorithm for genetic risk-scoring for major diseases across diverse ancestral populations. Their findings are published in Nature Genetics.

Although the algorithm is a start, and takes a logical approach to address health care disparities, it doesn't go far enough. Considering large groups – like Latinos or Africans – doesn't parse humanity sufficiently to hold much predictive power for genetic diseases, or conditions with large genetic components.

Tools to Track Disease: Biobanks to AI

To continue reading, go to DNA Science, where this post first appeared.

One of the most anticipated returns to normalcy following the pandemic is the in-person conference. Like the mythical Phoenix bird arising from the ashes, live get-togethers are finally replacing zoom life, bringing back the sharing of ideas and spontaneity that catalyzes insights and inspiration – especially in science and technology.

The Festival of Genomics and Biodata comes to the Boston Convention & Exhibition Center October 4-5. More than 150 speakers presenting in 7 "theaters" will cover a diversity of topics, plus round table discussions, "speed networking," and poster, career, and start-up "zones." Researchers, clinicians, and those working in drug discovery and development are welcome.

Front Line Genomics (FLG) is organizing the meeting. The best part? For 90 percent of participants, the conference is free! More than 2,000 attendees have already signed up. Register here.

To continue reading, go to DNA Science, where this post first appeared. 

I just used ChatGPT for the first time. Initially, I was concerned about my future as the chatbot near-instantaneously answered my queries on increasingly obscure terms from my field, genetics. Stumping the AI tool, however, took only about 10 minutes.

ChatGPT was released November 30, 2022, from OpenAI/Microsoft. "Chat Generative Pre-trained Transformer" is a little like Google on steroids. But after my brief encounter, I can't help but wonder whether it can handle the nuance, context, humor, and creativity of a human mind. Could it replace me as a textbook author?

My Career

I've been writing life science tomes for a long time. My favorite has always been Human Genetics: Concepts and Applications, the first edition published in 1994, at the dawn of the human genome sequencing era. The 14th edition published this week, from McGraw-Hill. A revision takes two years, one for updating and addressing reviewers' suggestions, another for "production," from copyediting through final pages. Then, a year off.

As genetics morphed into genomics, artificial intelligence stepped in, layering the combinatorial information of comparative genomics onto DNA sequences. Training on data sets and then searching for patterns could be used to deduce evolutionary trees depicting species relationships, in ancestry testing and forensics, and in identifying sequences of mutations that appear as a cancer spreads.

ChatGPT is too recent for me to have used it in revising the new edition, but I'm curious now. I could imagine it spitting out definitions, but a textbook is much more than "content." A human author adds perspective, experience, and perhaps knowledge beyond what ChatGPT can extract from the Internet.

To continue reading, go to DNA Science, where this post first appeared.

The Maui firestorm was so vast and fast that most identification of human remains will come from bits of persisting DNA from mitochondria.

The "Powerhouse of the Cell"

Most people likely last encountered mitochondria in high school biology class. The footprint-shaped "powerhouse of the cell" releases energy from breaking the chemical bonds that hold together nutrient molecules. The energy released in digesting food is held, fleetingly, in molecules of ATP, which serves as an energy debit card of sorts.

Each mitochondrion harbors its own tiny genome, a mere 36 genes compared to the 20,000 or so in a human cell's nucleus. And mitochondrial genes aren't just copies of nuclear ones – they're unique. Most encode enzymes that extract energy from ATP.

Mitochondria likely came from bacteria that single-celled organisms in ancient seas engulfed about 1.5 billion years ago. The idea is famous in biology as the endosymbiont theory. The bacteria in their new cellular homes, over time, retained some genes while surrendering others to the nucleus. And, gradually, the ancient bacteria evolved into mitochondria. Two recent reports in ScienceAdvances describe a contemporary contender for a descendant of the original stowaway bacterial genome that birthed mitochondria.

To continue reading, go to DNA Science, where this post first appeared.

As autumn looms, we're enjoying the last bites of sweet, juicy watermelon.

Conventional agriculture has molded our fruits and veggies to suit our palates, gradually crafting domesticated Citrullus lanatus from three ancestral melon species. But the process may have also removed valuable traits.

Researchers at the Boyce Thompson Institute in Ithaca, New York, have analyzed genomes of watermelon and its ancestors, revealing traits that early breeders may have inadvertently removed in their quest to maximize the red, sweet, watery flesh of the fruit. Their report appears in Plant Biotechnology Journal.

To continue reading, go to DNA Science, where this post first appeared.

The history of genetics begins, not with Gregor Mendel's pea experiments, but with people long ago noticing family resemblances and vulnerabilities so distinctive that shared environment alone can't explain them.

In the new literary fiction masterpiece The Covenant of Water, author-physician Abraham Verghese traces an unusual trait through three generations of a Christian family in India, against the historical backdrop of the coalescence of three states into Kerala, on the Malabar Coast, spanning 1900 to 1977. "The family … suffers a peculiar affliction: in every generation, at least one person dies by drowning – and in Kerala, water is everywhere," reads the jacket cover.

Through time, the drownings have been ascribed to bad luck and a familial recklessness, rather than to anything as cut in stone as an inherited condition. Frequent drownings seem more coincidence, harder to explain biologically than bleeding from missing a clotting factor or impaired breathing from cystic fibrosis. But the 700+ page tale is indeed about a rare manifestation of a rare condition.

The narrative captures the dread of an autosomal dominantly inherited disease, striking every generation, males and females. Dr. Verghese names all of the characters except the patriarch, who passed down the mutation behind the illness that isn't revealed until well into the saga. Perhaps keeping him nameless is a metaphor for the mysterious origin of what the family calls "the Condition."

To continue reading, go to DNA Science, where this post first appeared.

Determining the sequence of building blocks of entire genomes – aka genomics – first came to public attention in the 1990s, with the race to decode the first human genomes. Today, smartphones can carry our personal genome sequences.

Genomics applies to all species, revealing evolution in action, because we all use the same genetic code – that is, the correspondence between DNA sequences and the amino acid sequences of proteins. Many popular uses of "genetic code" actually mean "genome sequence."

Analysis of environmental DNA (eDNA) catalogs the DNA in specific places, from microorganisms inhabiting a human armpit to vast ecosystems. Several recent DNA Science posts describe eDNA:

A Glimpse of The Ocean's "Twilight Zone" Through Environmental DNA
A 2-million-year-old Ecosystem in the Throes of Climate Change Revealed in Environmental DNA
DNA in Strange Places: Hippo Poop, Zoo Air and Cave Dirt
Microbiome Analysis of Ancient Feces

Genome sequencing was critical from the start of COVID, as the first SARS-CoV-2 sequences were posted for researchers just days after initial case reports. That information led, thanks to vaccine shelved from the first SARS circa 2003, to the rapid development and deployment of mRNA vaccines against the new infectious disease.

To continue reading, go to DNA Science, where this post first appeared.

Humans aren't very good at regeneration — we can do it for skin, bone, and liver, but that's about it.

Flatworms, zebrafish, cockroaches, and salamanders can regenerate entire limbs. Yet even these abilities are unimpressive compared to those of Hydractinia symbiolongicarpus, aka a "squishy sea creature."

Only Simpler Animals Regenerate

Hydractinia, along with jellyfish, sea anemones, hydra, and  corals, are among 11,000 or so species in phylum Cnidaria, from the Greek cnidos for "stinging nettle." The tiny animals have soft bodies, circular symmetry, and sting. The hydractinia are among the most ancient of the Cnidaria. We last shared an ancestor with these animals more than 600 million years ago. They live in saltwater and are small and tube-shaped, clinging to hermit crabs.

To continue reading, go to DNA Science, where this post first appeared. 

Several recent reports are filling in the gaps of what we know about the earliest days and weeks of human prenatal development. Rather than attempting to image human embryos, researchers are tracking gene expression – that is, which genes a particular cell turns on or off at a particular time, providing a view of overall function.

The early embryos that are being investigated are donated by women undergoing assisted reproductive technologies, or are nurtured from induced pluripotent stem cells, which are created by culturing skin cells (fibroblasts) in a brew of growth factors. The stem cells divide and differentiate into early embryos, but with only partial supportive structures, like the amnion and placenta, so development ceases before the fetal period begins at 8 weeks after fertilization. The stem cells provide a Goldilocks solution, glimpsing early embryos, but not sustaining their development past a few weeks.

Three New Reports

To continue reading, go to DNA Science, where this post first appeared.

"If you're an adult with newly diagnosed non-small cell lung cancer that's spread and tests positive for PDL1 without an abnormal EGFR your first option could be …" announces a TV ad for a pair of targeted cancer drugs, flying by so fast that I doubt many patients can grasp anything.

According to the FDA, the wording of the ads comes from a "research team of social psychologists." Science journalists might better communicate drug mechanisms to consumers.

Another way to fathom the info in cancer drug ads is to go back to high school biology and consider the cell cycle – the molecular choreography that tells a cell whether, when, and how often to divide. The cycle has offshoots, called checkpoints, which enable a cell to die by apoptosis (aka programmed cell death) or pause for a time-out. Many targeted cancer drugs interrogate cell cycle enzymes and proteins that oversee checkpoints, stopping runaway cell division.

To continue reading, go to DNA Science, where this post first appeared.