Category Archives: Genome

Parents welcoming a new baby into their family are no longer content to count fingers and toes to assess their infant's state of health: In a survey released Thursday, nearly half said they would be "very" or "extremely" interested in having their newborn's genome sequenced, and fully a third more pronounced themselves "somewhat" interested.

Within 48 hours of a child's birth at Boston's Brigham and Women's Hospital, researchers gave 514 parents a brief orientation on the genome and its relevance for human health. They then asked how interested a parent would be in having his or her newborn's genome scanned and analyzed.

Interest was spread roughly evenly among parents regardless of their age, gender, race, ethnicity, level of education or family history of genetic disease. Whether a child was the firstborn in a family did not seem to influence a parent's propensity toward genetic sequencing.

But married parents and parents who had experienced health concerns about their baby were slightly less inclined to express interest in genomic sequencing for the child.

Where there were two parents available, they were surveyed separately about their interest. In 3 out of 4 such unions, parents were in agreement on their interest in genomic sequencing.

The study, published Thursday in the journal Genetics in Medicine, is the first to explore the attitudes of newborns' parents toward comprehensive genome testing. If it were a market-research tool, however, the study's findings would be good news for an initiative expected to be launched soon in Boston.

Lead author Dr. Robert C. Green, a geneticist at Brigham and Women's Hospital, and Alan Beggs of Boston Children's Hospital co-direct the BabySeq Project, which in 2015 is expected to offer several hundred parents of both sick and healthy newborns the opportunity to have their child's genome sequenced.

As genomic analysis has become cheaper, faster and increasingly revealing in terms of disease risk, the question of how routinely such scans should be conducted -- and who should have access to the results -- has been widely debated.

In March 2013, the American College of Medical Genetics and Genomics issued guidelines recommending that labs performing genome analysis for a specific health purpose search for a welter of readily-discernible genetic variations related to serious health problems, and report any such findings to the physician who ordered the test. Whether or not the patient wants or has asked for the unsought genomic findings, the group argued that physicians should pass any significant findings on to patients.

For children, however, genomic sequencing and all of its potential findings pose a dilemma. Younger minors are rarely thought capable of giving informed consent to receiving health information that may or may not turn out to be important.

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Most new parents might welcome having baby's genome sequenced

December 3rd - Jon Butterworth - Cosmic Genome Science Advent Calendar
Professor Jon Butterworth, from CERN and the Head of Physics at UCL fills us in on 2014 at the Large Hadron Collider. Every day a new free science clip from the good people at Cosmic Genome....

By: The Incomplete Map of the Cosmic Genome

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We examined highly differentiated SNPs between European and African populations, as well as among African populations to gain insights into loci that may have undergone selection in response to local adaptive forces (Supplementary Methods). To account for confounding due to Eurasian admixture, we also conducted analyses after masking Eurasian ancestry (Supplementary Methods and Supplementary Note 6).

On examining locus-specific EuropeAfrica differentiation, enrichment of loci known to be under positive selection was observed among the most differentiated sites (P = 1.41031). Furthermore, there was statistically significant enrichment for gene variants among these, indicating that this differentiation is unlikely to have arisen purely from random drift (P = 0.0002). Additionally, we found no evidence for background selection as the primary driver of differentiation among these loci (Supplementary Note 7).

In addition to genes known to be under positive selection (for example, SLC24A5, SLC45A2 and OCA219, 20, LARGE21 and CYP3A4/5) (Supplementary Fig. 3), we found evidence of differentiation in novel gene regions, including one implicated in malaria (for chemokine receptor 1, CR1) (Extended Data Fig. 8). CR1 carries the Knops blood group antigens and has previously been implicated in malaria susceptibility22 and severity23, with evidence suggesting positive selection in malaria-endemic regions24 (Extended Data Fig. 8). We also identified highly differentiated variants within genes involved in osmoregulation (ATP1A1 and AQP2) (Extended Data Fig. 8). Deregulation of AQP2 expression and loss-of-function mutations in ATP1A1 have been associated with essential and secondary hypertension, respectively25, 26. Climatic adaptive changes in these gene regions could potentially provide a biological basis for the high burden of hypertension and differences in salt sensitivity observed in SSA27.

In contrast, overall differentiation among African populations was modest (maximum masked FST = 0.19) (Supplementary Fig. 4) and only 56/1,237 sites remained in the tail distribution after masking (Supplementary Methods, Supplementary Table 6). This suggests that a large proportion of differentiation observed among African populations could be due to Eurasian admixture, rather than adaptation to selective forces (Supplementary Note 6). Genes known to be under selection were notably enriched among the most differentiated loci after masking of Eurasian ancestry (P = 2.31016). Among the 56 loci robust to Eurasian ancestry masking (Supplementary Table 6), we identified several loci known to be under selection (Extended Data Fig. 8), including a highly differentiated variant (rs1378940) in the CSK gene region implicated in hypertension in genome-wide association studies (GWAS)28. The major allele of rs1378940 among Africans was in complete linkage disequilibrium with the risk allele of the GWAS SNP rs1378942 (ref. 29), with the frequency of this allele highly correlated with latitude (r = 0.67), providing support for local adaptation in response to temperature as a possible mechanism for hypertension (Supplementary Fig. 5)30, 31.

Comparing populations residing in endemic and non-endemic infectious disease regions (Supplementary Methods), we identified several loci associated with infectious disease susceptibility and severity. As well as the known sickle-cell locus related to malaria, this approach identified additional signals for genes potentially under selection, including the PKLR region32, RUNX333, the haptoglobin locus, CD16334, IL1035, 36, CFH, and the CD28-ICOS-CLTA4 locus (Supplementary Table 7 and Extended Data Fig. 8)37. Similar comparisons for Lassa fever identified the known LARGE gene, as well as candidates associated with viral entry and immune response, including in the Histocompatibility Leukocyte Antigen region, DC-SIGN/DC-SIGNR38 (also known as CD209/CLEC4M), RNASEL, CXCR6, IFIH139 and OAS2/3 regions (Supplementary Table 7). For trypanosomiasis, we identified APOL140, as well as several loci implicated in immune response and binding to trypanosoma, including FAS, FASLG41, 42, IL23R43, SIGLEC6 and SIGLEC12 (Supplementary Table 7)44. For trachoma, we identified signals in ABCA1 and CXCR6, which may be important for the growth of the parasite and host immune response, respectively (Supplementary Table 7)45, 46.

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The African Genome Variation Project shapes medical genetics in Africa

A study published this week in Genetics in Medicine is the first to explore new parents' attitudes toward newborn genomic testing. The findings suggest that if newborn genomic testing becomes available, there would be robust interest among new parents, regardless of their demographic background.

The study, led by researchers at Brigham and Women's Hospital (BWH) and Boston Children's Hospital, found that the majority of parents surveyed were interested in newborn genomic testing.

As next-generation whole-exome and genome sequencing is integrated into clinical practice, researchers and clinicians are increasingly interested in genomic testing as a way to provide valuable personalized health information for newborns beyond what existing standard newborn genetic screening produces. But such testing, done shortly after birth, will require the interest and consent of new parents.

"Several other studies have measured parents' interest in newborn genomic screening, but none focused on new parents in the first 48 hours," said Robert C. Green, MD, MPH, a geneticist and researcher at BWH and Harvard Medical School and senior author of the study. "Since this is when genomic testing would be of the greatest value, it is especially important to study parents' attitudes immediately post-partum."

The researchers surveyed 514 parents at the well baby nursery at BWH within 48 hours of their child's birth. After receiving a brief orientation to the genome and its impacts on human health, 82.7 percent of parents reported being somewhat (36 percent), very, (28 percent) or extremely (18 percent) interested in newborn genomic testing. Results were similar regardless of parents' age, gender, race, ethnicity, level of education, family history of genetic disease, or whether or not the infant was a first-born child. Parents who had experienced concerns about the health of their newborn, however, were less likely to be interested in genomic testing.

The study was also the first to investigate whether asking parents about their interest in newborn genomic testing would cause them to reject existing, state-mandated newborn genetic screening (NBS), one of the most established and successful public health programs in the world.

"If even one parent had rejected it, that would have been a problem," said Susan Waisbren, PhD, lead author of the study and a psychologist and researcher in the Division of Genetics and Genomics at Boston Children's and Harvard Medical School. "But out of over 500 parents surveyed, not one of them questioned or rejected NBS."

The study was also the first to survey parents separately. Most couples were in agreement about their level of interest in newborn genomic testing.

"About 75 percent of couples were in concordance," Waisbren said. "This suggests that both parents should be involved when we are addressing concerns they may have about newborn genomic testing."

"Parents' strong interest in genomic screening for their newborns, as demonstrated by this study, underscores the importance of further research exploring the public health impacts of actually providing this testing," said Green, "particularly as it continues to become less expensive and more widely available."

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Genome sequencing for newborns: What do new parents think?

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The accomplishment through collaboration with Bayer CropScience could translate into better commercial varieties for growers.

Newswise A team of researchers at Texas Tech University, in collaboration with Bayer CropScience and the National Center for Genome Resources (NGCR) have developed a view into the structure of the cotton A-genome.

This is a significant accomplishment in the sequencing of the cotton genome, which will fuel multi-disciplinary basic and applied research to help increase cotton productivity.

This information will significantly advance cotton research worldwide, said Michael Galyean, dean of the College of Agricultural Sciences and Natural Resources. The genome sequence will eventually lead to improved cotton varieties containing environmentally friendly traits, which are preferred by producers, processors, manufacturers and consumers.

The annotated draft genome assembly being released is from the African/Asian species Gossypium arboreum, an extant representative of the cotton A-genome lineage paired with the D-genome lineage making up present day cultivated cottons. The A-genome species gave rise to spinnable fiber, eventually leading to the modern-day textile industry.

The draft sequence of G. arboreum is deposited in Genbank and is scheduled to be released to the public today.

Thea Wilkins, former professor of cotton genomics in Texas Techs Department of Plant and Soil Sciences, led the approach to unravel the genetic mystery of this species. She collaborated with scientists at Bayer CropScience and next-generation genomic sequencing technology and biocomputing providers KeyGene and NCGR.

This teams delivery of this high-quality genome sequence presents an unprecedented view into the structure of the A-genome, which will accelerate research efforts for improving cultivated cotton.

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Texas Tech's Sequencing of Cotton A-Genome Could Revolutionize Industry

December 1st - Robin Ince - Cosmic Genome Science Advent Calendar
Robin Ince invites you to stare in a mirror in the Dec 1st edition of the Cosmic Genome Science Advent Calendar. Every day a new free science clip from the good people at Cosmic Genome. Head...

By: The Incomplete Map of the Cosmic Genome

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December 1st - Robin Ince - Cosmic Genome Science Advent Calendar - Video

December 2nd - Sophie Scott - Cosmic Genome Science Advent Calendar
Professor Sophie Scott on the year #39;s research of laughter and rat related Nobels. Every day a new free science clip from the good people at Cosmic Genome. Head to cosmicgenome.com/advent...

By: The Incomplete Map of the Cosmic Genome

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December 2nd - Sophie Scott - Cosmic Genome Science Advent Calendar - Video

The Scientist just released its Top 10 innovations of the past year, and the major advances in genome sequencing that were developed in SoCal top that list.

1. DRAGEN Bio-IT Processor

This powerful processor speeds up sequencing time from 24 hours to 18 minutes, CEO Pieter van Rooyen said. According to The Scientist:

As genomic sequencing gets cheaper and more commonplace, the challenge becomes analyzing the avalanche of data that results. Typically, that responsibility falls to clusters of servers, which are bulky and energy-intensive to maintain. The DRAGEN Bio-IT Processor shrinks the physical bulk of genomic analysis to a chip that could be installed in a server the size of a desktop computer. The product also shrinks the cost of data analysis; Edico says users can save $6 million over four years by analyzing 18,000 whole genomes using DRAGEN.

We do all that processing in a much faster time, says Edicos president and CEO, Pieter van Rooyen. A genome that ordinarily takes 24 hours to analyze takes just 18 minutes with DRAGEN, according to Edico.

2. MiSeqDx

Illumina San Diego, California

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San Diego genome sequencing dominates The Scientists Top 10 Innovations

Spurs big man Tim Duncan, through his foundation, made a generous gift of $247,000 to the San Antonio Cancer Genome Project it was announced Monday.

The projects aim is to accelerate the development of new anticancer drugs; it was launched in 2012.

From the press release:

Like most people, Tim Duncan has been touched personally by cancer, and hopes for a cure for cancer in his lifetime. Duncan says he was drawn to the San Antonio 1000 Cancer Genome Project, because the information collected will ultimately be shared. [] The idea that a group of cancer researchers were willing to set aside egos, to make the information freely available and work strictly for the greater good of curing cancer was exactly the type of cancer project I was willing to support, Duncan said.

The projects founder is Dr. Anthony Tolcher, director of clinical research for START. [] I couldnt have been more surprised and grateful, said Dr. Tolcher, when presented with Tim Duncans donation. This gift will benefit the people of San Antonio and demonstrates the commitment that Mr. Duncan has to this city and the people of San Antonio.

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Tim Duncan Donates $247K to San Antonio 1000 Cancer Genome Project

NONCODING DNA REGIONS IN GENOME EVOLUTION

By: Walter Jahn

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NONCODING DNA REGIONS IN GENOME EVOLUTION - Video