How scientists are subtracting race from medical risk calculators

Posted in Articles, Health/Medicine/Genetics, Media Archive, United States on 2021-08-12 22:15Z by Steven

How scientists are subtracting race from medical risk calculators

Science Magazine
2021-07-22

Jyoti Madhusoodanan
Portland, Oregon


Anuj Shrestha

To pediatrician Nader Shaikh, the rhythm of treating babies running high fevers is familiar. After ruling out the obvious colds and other common viruses, he must often thread a catheter into a months-old baby to draw a urine sample and check for a urinary tract infection (UTI). “You have to hold the baby down, the baby’s crying, the mother is usually crying too,” says Shaikh, who works at the University of Pittsburgh. “It’s traumatic.”

UTIs, although relatively rare in children under age 2, carry a high risk of kidney damage in this group if left untreated. Often, the only symptom is a high fever. But high fevers can also signal a brain or blood infection, or a dozen other illnesses that can be diagnosed without a urine sample. To help clinicians avoid the unnecessary pain and expense of catheterizing a shrieking infant, Shaikh and his colleagues developed an equation that gauges a child’s risk of a UTI based on age, fever, circumcision status, gender, and other factors—including whether the child is Black or white. Race is part of the equation because previous studies found that—for reasons that aren’t clear—UTIs are far less common in Black children than in white ones.

The UTI algorithm is only one of several risk calculators that factor in race, which doctors routinely use to make decisions about patients’ care. Some help them decide what tests to perform next or which patients to refer to a specialist. Others help gauge a patient’s lung health, their ability to donate a liver or kidney, or which diabetes medicines they need.

In the past few years, however, U.S. doctors and students reckoning with racism in medicine have questioned the use of algorithms that include race as a variable. Their efforts gained momentum thanks to the Black Lives Matter movement. In August 2020, a commentary published in The New England Journal of Medicine (NEJM) highlighted the use of race in calculators as a problem “hidden in plain sight.” It’s widely agreed that race is a classification system designed by humans that lacks a genetic basis, says Darshali Vyas, a medical resident at Massachusetts General Hospital and co-author on the paper. “There’s a tension between that [understanding] and how we see race being used … as an input variable in these equations,” Vyas says. “Many times, there’s an assumption that race is relevant in a biological sense.”…

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“There is so much diversity in Africans that there is no such thing as an African race.”

Posted in Excerpts/Quotes on 2018-02-20 00:57Z by Steven

The study adds to established research undercutting old notions of race. You can’t use skin color to classify humans, any more than you can use other complex traits like height, [Sarah] Tishkoff says. “There is so much diversity in Africans that there is no such thing as an African race.”

Ann Gibbons, “New gene variants reveal the evolution of human skin color,” Science, October 12, 2017. http://www.sciencemag.org/news/2017/10/new-gene-variants-reveal-evolution-human-skin-color.

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New gene variants reveal the evolution of human skin color

Posted in Africa, Articles, Health/Medicine/Genetics, Media Archive on 2018-02-20 00:53Z by Steven

New gene variants reveal the evolution of human skin color

Science
2017-11-12

Ann Gibbons, Contributing Correspondent


Researchers have identified genes that help create diverse skin tones, such as those seen in the Agaw (left) and Surma (right) peoples of Africa.
ALESSIA RANCIARO & DR. SIMON R. THOMPSON

Most people associate Africans with dark skin. But different groups of people in Africa have almost every skin color on the planet, from deepest black in the Dinka of South Sudan to beige in the San of South Africa. Now, researchers have discovered a handful of new gene variants responsible for this palette of tones.

The study, published online this week in Science, traces the evolution of these genes and how they traveled around the world. While the dark skin of some Pacific Islanders can be traced to Africa, gene variants from Eurasia also seem to have made their way back to Africa. And surprisingly, some of the mutations responsible for lighter skin in Europeans turn out to have an ancient African origin.

“This is really a landmark study of skin color diversity,” says geneticist Greg Barsh of the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama.

Researchers agree that our early australopithecine ancestors in Africa probably had light skin beneath hairy pelts. “If you shave a chimpanzee, its skin is light,” says evolutionary geneticist Sarah Tishkoff of the University of Pennsylvania, the lead author of the new study. “If you have body hair, you don’t need dark skin to protect you from ultraviolet [UV] radiation.”

Until recently, researchers assumed that after human ancestors shed most body hair, sometime before 2 million years ago, they quickly evolved dark skin for protection from skin cancer and other harmful effects of UV radiation. Then, when humans migrated out of Africa and headed to the far north, they evolved lighter skin as an adaptation to limited sunlight. (Pale skin synthesizes more vitamin D when light is scarce.)…

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Loci associated with skin pigmentation identified in African populations

Posted in Africa, Articles, Health/Medicine/Genetics, Media Archive on 2017-12-04 01:50Z by Steven

Loci associated with skin pigmentation identified in African populations

Science
2017-10-12
eaan8433
DOI: 10.1126/science.aan8433

Nicholas G. Crawford, Derek E. Kelly, Matthew E. B. Hansen, Marcia H. Beltrame, Shaohua Fan, Shanna L. Bowman, Ethan Jewett, Alessia Ranciaro, Simon Thompson, Yancy Lo, Susanne P. Pfeifer, Jeffrey D. Jensen, Michael C. Campbell, William Beggs, Farhad Hormozdiari, Sununguko Wata Mpoloka, Gaonyadiwe George Mokone, Thomas Nyambo, Dawit Wolde Meskel, Gurja Belay, Jake Haut, NISC Comparative Sequencing Program, Harriet Rothschild, Leonard Zon, Yi Zhou, Michael A. Kovacs, Mai Xu, Tongwu Zhang, Kevin Bishop, Jason Sinclair, Cecilia Rivas, Eugene Elliot, Jiyeon Choi, Shengchao A. Li, Belynda Hicks, Shawn Burgess, Christian Abnet, Dawn E. Watkins-Chow, Elena Oceana, Yun S. Song, Eleazar Eskin, Kevin M. Brown, Michael S. Marks, Stacie K. Loftus, William J. Pavan, Meredith Yeager, Stephen Chanock, Sarah Tishkoff

Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2 and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in southern Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of UV response genes under selection in Eurasians.

Variation in epidermal pigmentation is a striking feature of modern humans. Human pigmentation is correlated with geographic and environmental variation (Fig. 1). Populations at lower latitudes have darker pigmentation than populations at higher latitudes, suggesting that skin pigmentation is an adaptation to differing levels of ultraviolet radiation (UVR) (1). Because equatorial regions receive more UVR than temperate regions, populations from these regions (including sub-Saharan Africans, South Asians, and Australo-Melanesians) have darker pigmentation (Fig. 1), which likely mitigates the negative impact of high UVR exposure such as skin cancer and folate degradation (1). In contrast, the synthesis of vitamin D3 in response to UVR, needed to prevent rickets, may drive selection for light pigmentation at high latitudes (1).

The basal layer of human skin contains melanocytes, specialized pigment cells that harbor subcellular organelles called melanosomes in which melanin pigments are synthesized and stored and then transferred to keratinocytes (2). Melanosome morphology and content differs between melanocytes that synthesize mainly eumelanins (black-brown pigments) or pheomelanins (pigments which range from yellow to reddish-brown) (3). Variation in skin pigmentation is due to the type and quantity of melanins generated, melanosome size, and the manner in which keratinocytes sequester and degrade melanins (4).

While over 350 pigmentation genes have been identified in animal models, only a subset of these genes have been linked to normal variation in humans (5). Of these, there is limited knowledge about loci that affect pigmentation in populations with African ancestry (6, 7).

Skin pigmentation is highly variable within Africa

To identify genes affecting skin pigmentation in Africa, we used a DSM II ColorMeter to quantify light reflectance from the inner arm as a proxy for melanin levels in 2,092 ethnically and genetically diverse Africans living in Ethiopia, Tanzania, and Botswana (table S1 and figs. S1 and S2) (8). Skin pigmentation levels vary extensively among Africans, with darkest pigmentation observed in Nilo-Saharan speaking pastoralist populations in Eastern Africa and lightest pigmentation observed in San hunter-gatherer populations from southern Africa (Fig. 2 and table S1)…

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Departure of U.S. Census director threatens 2020 count

Posted in Articles, Census/Demographics, Media Archive, Politics/Public Policy, United States on 2017-05-11 02:01Z by Steven

Departure of U.S. Census director threatens 2020 count

Science
2017-05-09

Jeffrey Mervis


John Thompson will leave the Census Bureau on 30 June. U.S. Census Bureau

John Thompson is stepping down next month as director of the U.S. Census Bureau. His announcement today comes less than 1 week after a congressional spending panel grilled him about mounting problems facing the agency in preparing for the 2020 decennial census. And Thompson’s pending retirement is weighing heavily on the U.S. statistical community.

Thompson is leaving halfway through a 1-year extension of a term that expired last December. His departure will create what a 2011 law was expressly designed to avoid—a leadership vacuum during a crucial time in the 10-year life cycle of the census, the nation’s largest civilian undertaking. The immediate concern is who the Trump administration will appoint, and how soon it will act…

Ken Prewitt, who led the agency from 1998 to 2001, worries that a long delay in naming a well-qualified replacement for Thompson could be the first step of a long, steep decline in the quality of the federal statistic system, which spans 13 agencies. “That system is fragile, and it wouldn’t take much to damage it severely,” says Prewitt, a professor of social affairs at Columbia University. “My real fear is that they don’t care enough to do a good job with the 2020 census. And then after doing a bad job, they decide to let the private sector take over.”…

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Taking race out of human genetics

Posted in Articles, Health/Medicine/Genetics, Media Archive, Politics/Public Policy, Social Science on 2016-02-06 17:35Z by Steven

Taking race out of human genetics

Science
Volume 351, Issue 6273 (2016-02-05)
pages 564-565
DOI: 10.1126/science.aac4951

Michael Yudell, Associate Professor
Dornsife School of Public Health Department of Community Health and Prevention
Drexel University, Philadelphia, Pennsylvania

Dorothy Roberts, George A. Weiss University Professor of Law and Sociology and the Raymond Pace and Sadie Tanner Mossell Alexander Professor of Civil Rights
University of Pennsylvania

Rob DeSalle, Curator, Molecular Systematics; Principal Investigator, SICG Genomics Lab; Professor, Richard Gilder Graduate School
American Museum of Natural History, New York, New York

Sarah Tishkoff, David and Lyn Silfen University Professor in Genetics and Biology
University of Pennsylvania

In the wake of the sequencing of the human genome in the early 2000s, genome pioneers and social scientists alike called for an end to the use of race as a variable in genetic research (1, 2). Unfortunately, by some measures, the use of race as a biological category has increased in the postgenomic age (3). Although inconsistent definition and use has been a chief problem with the race concept, it has historically been used as a taxonomic categorization based on common hereditary traits (such as skin color) to elucidate the relationship between our ancestry and our genes. We believe the use of biological concepts of race in human genetic research—so disputed and so mired in confusion—is problematic at best and harmful at worst. It is time for biologists to find a better way.

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How Europeans evolved white skin

Posted in Articles, Europe, Health/Medicine/Genetics, Media Archive on 2015-04-06 01:26Z by Steven

How Europeans evolved white skin

Science
2015-04-02
DOI: 10.1126/science.aab2435

Ann Gibbons, Contributing Correspondent

ST. LOUIS, MISSOURI—Most of us think of Europe as the ancestral home of white people. But a new study shows that pale skin, as well as other traits such as tallness and the ability to digest milk as adults, arrived in most of the continent relatively recently. The work, presented here last week at the 84th annual meeting of the American Association of Physical Anthropologists, offers dramatic evidence of recent evolution in Europe and shows that most modern Europeans don’t look much like those of 8000 years ago.

The origins of Europeans have come into sharp focus in the past year as researchers have sequenced the genomes of ancient populations, rather than only a few individuals. By comparing key parts of the DNA across the genomes of 83 ancient individuals from archaeological sites throughout Europe, the international team of researchers reported earlier this year that Europeans today are a mix of the blending of at least three ancient populations of hunter-gatherers and farmers who moved into Europe in separate migrations over the past 8000 years. The study revealed that a massive migration of Yamnaya herders from the steppes north of the Black Sea may have brought Indo-European languages to Europe about 4500 years ago.

Now, a new study from the same team drills down further into that remarkable data to search for genes that were under strong natural selection—including traits so favorable that they spread rapidly throughout Europe in the past 8000 years. By comparing the ancient European genomes with those of recent ones from the 1000 Genomes Project, population geneticist Iain Mathieson, a postdoc in the Harvard University lab of population geneticist David Reich, found five genes associated with changes in diet and skin pigmentation that underwent strong natural selection…

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People from Mexico show stunning amount of genetic diversity

Posted in Articles, Caribbean/Latin America, Health/Medicine/Genetics, Media Archive, Mexico on 2014-06-16 13:58Z by Steven

People from Mexico show stunning amount of genetic diversity

Science
2014-06-12

Lizzie Wade, Latin America Correspondent

Imagine if people from Kansas and California were as genetically distinct from each other as someone from Germany is from someone from Japan. That’s the kind of remarkable genetic variation that scientists have now found within Mexico, thanks to the first fine-scale study of human genetic variation in that country. This local diversity could help researchers trace the history of the country’s different indigenous populations and help them develop better diagnostic tools and medical treatments for people of Mexican descent living all over the world.

The team has done a “tremendous job” of creating a “blueprint of all the genetic diversity in Mexico,” says Bogdan Pasaniuc, a population geneticist at the University of California (UC), Los Angeles, who was not involved in the research…

…When the team analyzed the genomes of 511 indigenous individuals from all over Mexico, they found a striking amount of genetic diversity. The most divergent indigenous groups in Mexico are as different from each other as Europeans are from East Asians, they report online today in Science. This diversity maps onto the geography of Mexico itself. The farther away ethnic groups live from each other, the more different their genomes turn out to be.

But most people in Mexico or of Mexican descent these days are not indigenous but rather mestizo, meaning they have a mixture of indigenous, European, and African ancestry. Do their genomes also vary by what region of Mexico they come from, or has all that local variation been smoothed out by centuries of different groups meeting, mixing, and having babies?…

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Geneticists and the Biology of Race Crossing

Posted in Articles, Health/Medicine/Genetics, Media Archive, Social Science on 2013-10-20 00:35Z by Steven

Geneticists and the Biology of Race Crossing

Science Magazine
Volume 182, Number 4114 (1973-11-23)
pages 790-796
DOI: 10.1126/science.182.4114.790

William B. Provine, Andrew H. and James S. Tisch Distinguished University Professor
Cornell University

Geneticists changed their minds about the biological effects of race crossing

Geneticists in England and the United States clearly reversed their published remarks on the effects of race crossing between 1930 and 1950. The reversal occurred in two steps. First came the change in the 1930’s from a condemnation of wide race crosses to an agnostic view. The second change, from the agnostic view to the belief that wide race crosses were at worst biologically harmless, took place during and shortly after World War II.

The entire reversal occurred in the light of little new compelling data from studies of actual human race crosses. The lack of new data is unsurprising. Few geneticists wished to initiate experiments that took three human generations to complete. And controlled race crosses are hard to arrange, even with government grants. What might be more surprising was the willingness of geneticists to make such positive statements about race crossing when they had so little reliable genetic evidence.

I interviewed or wrote to ten prominent geneticists who worked on human genetics between 1930 and 1950. Not one believed that new evidence on race crossing was the primary reason why geneticists changed their minds about the effects of race crossing. One plausible explanation, that the rise of “population thinking” (44) caused geneticists to change their minds, does not fit the evidence. Castle was no more of a “population” thinker than East, yet they differed radically in their conclusions about race crossing. What, then, did cause geneticists to change their minds?

Most important was the revulsion of educated people in the United States and England to Nazi race doctrines and their use in justifying extermination of Jews. Few geneticists wanted to argue, as had the Nazis, that biology showed race crossing was harmful. Instead, having witnessed the horrible toll, geneticists naturally wanted to argue that biology showed race crossing was at worst harmless. No racist nation could misuse that conclusion. And geneticists did revise their biology to fit their feelings of revulsion.

Geneticists’ ideas about the related question of hereditary mental differences between races is perhaps undergoing a similar development to that seen earlier in their ideas about race crossing. In 1951, judging from the response to the Unesco second statement on race and comments in genetics literature, most geneticists agreed with Muller that races probably differed in significant average mental traits. By 1969, when Arthur Jensen advocated this view in his controversial article (45), most geneticists who spoke publicly on the issue had adopted an agnostic position. Knowledge of hereditary racial differences in IQ had scarcely changed since 1951, but society had changed considerably in racial attitudes. It will be interesting to see if during the next several decades geneticists will argue, on the basis of little additional evidence, that hereditary mental differences between races do not exist.

I am not condemning geneticists because social and political factors have influenced their scientific conclusions about race crossing and race differences. It is necessary and natural that changing social attitudes will influence areas of biology where little is known and the conclusions are possibly socially explosive. The real danger is not that biology changes with society, but that the public expects biology to provide the objective truth apart from social influences. Geneticists and the public should realize that the science of genetics is often closely intertwined with social attitudes and political considerations…

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Use of Blood Groups in Human Classification

Posted in Anthropology, Articles, Health/Medicine/Genetics, Media Archive on 2012-02-10 04:30Z by Steven

Use of Blood Groups in Human Classification

Science Magazine
Volume 112, Number 2903 (1950-08-18)
pages 187-196
DOI: 10.1126/science.112.2903.187

William C. Boyd
Boston University School of Medicine, Boston, Massachusetts

—Will he not fancy that the shadows which he formerly saw are truer than the objects which are now shown to him!
Plato, The Republic

In recent years there has been an increasing feeling, on the part of both geneticists and physical anthropologists, that genetical methods ought to be applied to the problems of the classification of man, and a number of proposals to this effect have been made. Nevertheless, new books of anthropology, as they have been published, have been found to contain much the same old classifications based on morphological characteristics, skin color, etc., even though the authors may have started with the announced intention of making use of the newer methods. It is clear that many a worker, attempting to apply genetical methods of taxonomy to man, has been disappointed, and, in fact, one scientist, formerly quite active in the field of physical anthropology, has now given it up, and announced in a letter to me: “I tried to see what blood groups would tell me about ancient man, and found the results very disappointing.”

A careful analysis of the situation will show that such disappointment is based largely on two circumstances. First, there is the fact that the blood grouping genes affect invisible serological characteristics of the individual, and are thus never visible to the naked eye. It is to be feared that we are all too much inclined to be impressed by the visible as opposed to the invisible. Second, there is the fact that the layman’s concept of race (which is that the human species can be divided up by valid, scientific methods, into various groups that are pretty different from each other and which will look pretty different from each other) has been unconsciously retained by many scientific workers, and the hypothetical dissenting readers are unconsciously expecting that the new system we propose to introduce will also provide us with startling differences in the appearance and behavior of the different “races” we define, and will feel let down to discover that the new classification does not, when all is said about it, reveal any very dramatic results.

If the blood grouping genes had affected, not characteristics of the blood, but prominent morphological or physical characteristics such as the shape of the head, color of the skin, etc., there cannot be the slightest question that they would already have been made the chief basis of a racial classification and would have been considered entirely adequate for that purpose.

Equivalence of Genes

From our knowledge of genetics we may see that there is nothing fundamentally different between the blood grouping genes as genes, and the genes which do affect morphological features. It is simply a historical accident that fairly adequate information was obtained about the mode of transmission of blood grouping genes before any information at all equivalent in amount or value was obtained about the genes affecting physical appearance.

In view of these facts, and since there seems to be no reason to suppose that the location of a gene in a chromosome, or the nature of the particular chromosome in which the gene resides, determines in advance the main or even the subsidiary characteristics which are to be influenced by the gene, it might be instructive to let our imaginations roam a bit. The outwardly observable effects of the blood group genes are, so far as we know, zero. Therefore let us make some arbitrary assumptions as to the sort of effect which the blood grouping genes could have produced, supposing them to have affected some of the external and visible char-…

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