Breaking News
December 10, 2018 - Scientists find answers to how cancer spreads
December 10, 2018 - Study explores why older people read more slowly
December 10, 2018 - Asbestos found in most NHS hospitals finds BBC inquiry
December 10, 2018 - Researchers use new technique to probe hydrogen bonds
December 10, 2018 - Music improves social communication in autistic children
December 10, 2018 - Some Brain Tumors May Respond to Immunotherapy, New Study Suggests
December 10, 2018 - Banning junk food ads to combat childhood obesity
December 10, 2018 - Skin Autofluorescence Predicts T2DM, Heart Disease, Mortality
December 10, 2018 - Largest autism sequencing study to date yields 102 genes associated with ASD
December 10, 2018 - Statins associated with low risk of side effects
December 10, 2018 - Study explores how schools address adolescent self-harming practices
December 10, 2018 - Pregnancy in adolescence linked to increased risks of complications in young mothers
December 10, 2018 - Risk Analysis publishes special issue on communicating about Zika virus
December 10, 2018 - Botox May Help Prevent Post-Op A-Fib
December 10, 2018 - African-American mothers rate boys higher for ADHD
December 10, 2018 - Graphic warning labels cancel out cigarettes’ appeal to young people
December 10, 2018 - Australian researchers to study gas inhalational anaesthetic and likelihood of cancer return
December 10, 2018 - Individual neurons located within the brain have implications for psychiatric diseases
December 10, 2018 - Researchers improve bariatric surgery scoring system to extend prediction time for diabetic remission
December 10, 2018 - HPV type 16 or 18 associated with cervical cancer risk in young women
December 10, 2018 - Cervical cancer risk is higher in women with positive HPV, but no cellular abnormalities
December 10, 2018 - Combo therapy not needed if low RA disease activity achieved
December 10, 2018 - Novel therapeutic targets based on biology of aging show promise for Alzheimer’s disease
December 10, 2018 - UC San Diego professor receives NCI Outstanding Investigator Award for cancer research
December 10, 2018 - Study evaluates placental mesenchymal stem cell sheets for myocardial repair and regeneration
December 10, 2018 - Blueprint Medicines Announces Updated Results from Ongoing EXPLORER Clinical Trial of Avapritinib Demonstrating Broad Clinical Activity and Significant Symptom Reductions in Patients with Systemic Mastocytosis
December 10, 2018 - Study clarifies ApoE4’s role in dementia
December 10, 2018 - Eating disorders now a top priority with Australian Government
December 10, 2018 - Neuronal activity in the brain allows prediction of risky or safe decisions
December 10, 2018 - FDA Alerts Health Care Professionals and Patients Not to Use Drug Products Intended to be Sterile from Promise Pharmacy
December 10, 2018 - Improving dementia care and treatment saves thousands of pounds in care homes
December 10, 2018 - Heroin-assisted treatment can offer benefits, reduce harms
December 10, 2018 - People covered by Michigan’s expanded Medicaid program report improvements in health, finds study
December 10, 2018 - Hazelnuts improve micronutrient levels in older adults
December 9, 2018 - History of Partner Violence Tied to Menopause Symptoms
December 9, 2018 - Clean Up Safely After a Disaster|Natural Disasters and Severe Weather
December 9, 2018 - Drug wholesalers drove fentanyl’s deadly rise, report concludes
December 9, 2018 - Deprescribing could help manage polypharmacy in older adults
December 9, 2018 - Retraction of article “Joy of cooking too much” from journal
December 9, 2018 - FDA Warns of Rare Stroke Risk With MS Drug Lemtrada (Alemtuzumab)
December 9, 2018 - Feds say heroin, fentanyl remain biggest drug threat to US
December 9, 2018 - Eliminating microglia can reverse some aspects of stress sensitization, study shows
December 9, 2018 - New genetic insight could help treat rare debilitating heart and lung condition
December 9, 2018 - MiRagen Therapeutics Announces Final Safety, Biodistribution and Clinical Efficacy Data From Phase 1 Cobomarsen Clinical Trial in Patients With Mycosis Fungoides
December 9, 2018 - Work with your doctor to weigh pros, cons of treatment options for hyperthyroidism
December 9, 2018 - CWRU researcher secures $14.6 million funding for genetic study into Alzheimer’s disease
December 9, 2018 - High intensity statin treatment and adherence could save more lives
December 9, 2018 - Surgery patients use only 1/4 of prescribed opioids, and prescription size matters
December 9, 2018 - AXT offers Phi Optics upgrade to QPI systems for inverted light microscopes
December 9, 2018 - New booklet could help improve conditions of young pupils with albinism
December 9, 2018 - Few Physicians Work in Practices That Use Telemedicine
December 9, 2018 - Older Adults and Oral Health
December 9, 2018 - Health utility values improve after septorhinoplasty
December 9, 2018 - New EU-funded project provides insight into how the brain develops
December 9, 2018 - Expanded use of tele-emergency services can help strengthen rural hospitals
December 9, 2018 - Infections in the Young May Be Tied to Risk for Mental Illness: Study
December 9, 2018 - Profile: Native Hawaiians and Pacific Islanders
December 9, 2018 - Snoring poses greater cardiac risk to women
December 9, 2018 - Researcher takes further steps in understanding how and why cute aggression occurs
December 9, 2018 - Researchers create new light-activated tools for controlling neurons
December 9, 2018 - Spinal cord injury disrupts the body’s internal clock, study shows
December 9, 2018 - Babies recognize nested structures similar to our grammar
December 9, 2018 - UT Austin researcher receives $2.5 million CZI grant for neurodegenerative disease research
December 9, 2018 - Sleep problems found to be prevalent and increasing among college students
December 9, 2018 - Study reveals why some children are susceptible to the effects of maltreatment
December 9, 2018 - Study investigates influence of different opioids on driving performance
December 9, 2018 - Jazz Pharmaceuticals Announces First Patient Enrolled in Phase 3 Clinical Trial Evaluating JZP-258 for the Treatment of Idiopathic Hypersomnia
December 9, 2018 - Eliminating microglia prevents heightened immune sensitivity after stress
December 9, 2018 - Boys with social difficulties are at greatest risk of early substance use
December 9, 2018 - ‘Wrong’ connective tissue cells linked to worse prognosis in breast cancer patients
December 8, 2018 - Chronic, refractory schizophrenia patients benefit from targeted cognitive training
December 8, 2018 - Advertising in kids’ apps more prevalent than parents may realize
December 8, 2018 - New way to trace the transmission histories of rare genetic diseases
December 8, 2018 - ASH: A+CHP Bests CHOP for Peripheral T-Cell Lymphoma
December 8, 2018 - Results of pediatric genomic epilepsy tests often reclassified
December 8, 2018 - New way of controlling HIV latency to completely eradicate the virus
December 8, 2018 - Phasefocus to showcase the Livecyte 2 at ASCB
December 8, 2018 - KHN’s ‘What the Health?’ Is health spending the next big political issue?
December 8, 2018 - Mussels take in microplastic pollution fibers and flush most of them out again
December 8, 2018 - AHA: How to Stop Smoking … for Good
About 300 million bits of DNA are missing from basic reference genome, report scientists

About 300 million bits of DNA are missing from basic reference genome, report scientists

image_pdfDownload PDFimage_print

For the past 17 years, most scientists around the globe have been using the nucleic acid sequence, or genome, an assembly of DNA information, from primarily a single individual as a kind of “baseline” reference and human species representation for comparing genetic variety among groups of people.

Known as the GRCh38 reference genome, it is periodically updated with DNA sequences from other individuals, but in a new analysis, Johns Hopkins scientists now say that the collective genomes of 910 people of African descent have a large chunk — about 300 million bits — of genetic material that is missing from the basic reference genome.

“There’s so much more human DNA than we originally thought,” says

Knowing the variations in genomes across populations is essential to research design to reveal why certain people or groups of people may be more or less susceptible to common health conditions, such as heart disease, cancer and diabetes, and Salzberg says that scientists need to build more reference genomes that more closely reflect different populations.

“The whole world is relying on what is essentially a single reference genome, and when a particular DNA analysis doesn’t match the reference and you throw away those non-matching sequences, those discarded bits may in fact hold the answers and clues you are seeking,” says Salzberg.

Rachel Sherman, the first author on the report and a Ph.D. student in computer science at Johns Hopkins, says, “If you are a scientist looking for genome variations linked to a condition that is more prevalent in a certain population, you’d want to compare the genomes to a reference genome more representative of that population.”

Specifically, the world’s reference genome was assembled from the nucleic acid sequences of a handful of anonymous volunteers. Other researchers later determined that 70 percent of the reference genome derives from a single individual who was half European and half African, and the rest derives from multiple individuals of European and Chinese descent, according to Salzberg.

“These results underscore the importance of research on populations from diverse backgrounds and ancestries to create a comprehensive and inclusive picture of the human genome,” said James P. Kiley, Ph.D., director of the Division of Lung Diseases at the National Heart, Lung, and Blood Institute (NHLBI), which supported the study. “A more complete picture of the human genome may lead to a better understanding of variations in disease risk across different populations.”

For the new analysis, described online Nov. 19 in Nature Genetics, Salzberg and Sherman began their project with DNA collected from 910 individuals of African descent who live in 20 regions around the globe, including the U.S., Central Africa and the Caribbean. Their DNA had been collected for an NHLBI-supported study at Johns Hopkins led by Kathleen Barnes, Ph.D., who is now at the University of Colorado and continues to lead this program on genetic factors that may contribute to asthma and allergy, conditions known to be overrepresented in this population.

Many researchers look for small differences between the reference genome and the genomes of the individuals they are studying — sometimes only a single change in chemical base pairs within the DNA. These small changes are called single nucleotide polymorphisms, or SNPs.

However, Salzberg’s team focuses on larger variations in the genome. “SNPs correlate really well to figure out an individual’s ancestry, but they haven’t worked as well to determine genetic variations that may contribute to common conditions and diseases,” says Salzberg. “Some conditions may be due to variations across larger sections of the genome.”

Over a two-year period, Salzberg and Sherman analyzed the DNA sequences of the 910 people, looking for sections of DNA at least 1,000 base pairs long that did not align with or match the reference genome. “Within these DNA sequences are what makes one individual unique,” says Sherman.

They assembled those sequences and looked for overlaps and redundancies, filtering out sequences shorter than 1,000 base pairs, and DNA likely linked to bacteria, which is found in all humans.

Then they compared the assembled sequences of all 910 individuals to the standard reference genome to find what Salzberg calls, “chunks of DNA that you may have and I don’t.”

In all, they found 300 million base pairs of DNA — which is about 10 percent of the estimated size of the entire human genome — that the reference genome did not account for. The largest section of unique DNA they found was 152,000 base pairs long, but most chunks were about 1,000-5,000 base pairs long.

A small portion of these DNA sequences may overlap with genes that encode proteins or other cellular functions, but, Salzberg says, they have not mapped the function of each sequence.

They also failed to find sequences that aligned with having asthma or not. But Salzberg isn’t deterred: “Until you survey the landscape, you can’t figure out what’s useful.”

Source:

https://www.hopkinsmedicine.org/news/newsroom/news-releases/widely-used-reference-for-the-human-genome-is-missing-300-million-bits-of-dna

Tagged with:

About author

Related Articles