Breaking News
February 18, 2019 - How Inactivity and Junk Food Can Harm Your Brain
February 18, 2019 - Diabetes tops common conditions for frequent geriatric emergency patients
February 18, 2019 - Longer-lived sperm produces offspring with healthier lifespans
February 18, 2019 - New dental adhesive prevents tooth decay around orthodontic brackets
February 18, 2019 - New eHealth tool shows potential to improve quality of asthma care
February 18, 2019 - New Australian initiative helps emergency clinicians to improve patient care
February 17, 2019 - Apellis Pharmaceuticals’ APL-2 Receives Fast Track Designation from the FDA for the Treatment of Patients with Paroxysmal Nocturnal Hemoglobinuria
February 17, 2019 - Researchers identify faulty ‘brake’ that interferes with heart muscle’s ability to contract and relax
February 17, 2019 - Support from trusted adults can reduce risk of dying in suicidal teens, finds study
February 17, 2019 - Heart attack awareness improved since 2008
February 17, 2019 - Exercise gives a better brain boost to older men than women
February 17, 2019 - New research disproves previous assumptions of how looks influence personality
February 17, 2019 - Cannabis use as a teenager linked to depression later in life
February 17, 2019 - Sinks by Toilets in ICU Patient Rooms Harbor Harmful Bacteria
February 17, 2019 - Cancer cells’ plasticity makes them harder to stop
February 17, 2019 - Young cannabis users have increased risk of depression and suicidal behavior
February 17, 2019 - Tasmanian Devils Likely to Survive Cancer Scourge
February 17, 2019 - Neoadjuvant PD-1 blockade seems effective in glioblastoma
February 17, 2019 - Personal, social factors play role in enabling sustainable return to work after ill health
February 17, 2019 - Mouse studies show ‘inhibition’ theory of autism wrong
February 17, 2019 - Study shows how neuroactive steroids inhibit activity of pro-inflammatory proteins
February 17, 2019 - Use of liver grafts from older donors decreased despite better outcomes in recipients
February 17, 2019 - MUSC researchers discover new mechanism for a class of anti-cancer drugs
February 17, 2019 - HPV misconceptions are causing women to miss smear tests
February 17, 2019 - Sanofi and Regeneron Offer Praluent (alirocumab) at a New Reduced U.S. List Price
February 17, 2019 - Researchers say auditory testing can identify children for autism screening
February 17, 2019 - New method analyzes how single biological cells react to stressful situations
February 17, 2019 - WVU gynecologic oncologist investigates novel treatment for cervical and vaginal cancers
February 17, 2019 - ADHD diagnoses poorly documented
February 17, 2019 - Majority of gender minority youth do not identify with traditional sexual identity labels
February 17, 2019 - AbbVie, Teneobio enter into strategic transaction to develop potential treatment for multiple myeloma
February 17, 2019 - Lower Birth Weight May Up Risk for Psychiatric Disorders
February 17, 2019 - Scientists identify reversible molecular defect underlying rheumatoid arthritis
February 17, 2019 - Moffitt researchers shed light on how CAR T cells function mechanistically
February 16, 2019 - Female Anatomy May Play Big Role in Sperm’s Success
February 16, 2019 - BMI may mediate inverse link between fiber intake, knee OA
February 16, 2019 - Movement impairments in autism can be reversed through behavioral training
February 16, 2019 - Studies address racial disparities in postpartum period and cardiovascular health
February 16, 2019 - Scientists implicate hidden genes in the severity of autism symptoms
February 16, 2019 - Decreased deep sleep linked to early signs of Alzheimer’s disease
February 16, 2019 - Neuroscientists show how the brain responds to texture
February 16, 2019 - Gilead Announces Topline Data From Phase 3 STELLAR-4 Study of Selonsertib in Compensated Cirrhosis (F4) Due to Nonalcoholic Steatohepatitis (NASH)
February 16, 2019 - What Can I Do About Sweating? (for Teens)
February 16, 2019 - Companies navigate dementia conversations with older workers
February 16, 2019 - Newly developed stem cell technologies show promise for treating PD patients
February 16, 2019 - Collaborative material research could advance self-assembling nanomaterials
February 16, 2019 - Researchers take major step in creating technology that mimics the human brain
February 16, 2019 - Erasing memories associated with cocaine use reduces drug seeking behavior
February 16, 2019 - Artificial intelligence can accurately predict prognosis of ovarian cancer patients
February 16, 2019 - Racial disparities in cancer deaths on the decline for America
February 16, 2019 - FDA authorizes new interoperable insulin pump for children, adults with diabetes
February 16, 2019 - Coexisting Medical Conditions, Smoking Explain PTSD-CVD Link
February 16, 2019 - Skin Cancer Screening: MedlinePlus Lab Test Information
February 16, 2019 - ‘Happiness’ exercises can boost mood in those recovering from substance use disorder
February 16, 2019 - Cell manipulation could soon halt or reverse aging
February 16, 2019 - Pumped Breast Milk Falls Short of Breastfed Version
February 16, 2019 - Men’s porn habits could fuel partners’ eating disorders, study suggests
February 16, 2019 - Rapid progression of age-related diseases may result from formation of vicious cycles
February 16, 2019 - Immune checkpoint molecule protects against future development of cancer
February 16, 2019 - New method produces hydrogels that have properties similar to cells’ environment
February 16, 2019 - $4.1 million funding for heart research on Valentine’s Day
February 16, 2019 - General anesthesia in early infancy unlikely to have lasting effects on developing brains
February 16, 2019 - New breakthroughs for muscular dystrophy research
February 16, 2019 - First Opinion: Embryo editing for higher IQ is a fantasy. Embryo profiling for it is almost here
February 16, 2019 - Vapers develop cancer-related gene deregulation as cigarette smokers
February 16, 2019 - Bringing Antimicrobial Susceptibility Testing (AST) to the Community
February 16, 2019 - Decolonization protocol after hospital discharge can prevent dangerous infections
February 16, 2019 - Children with ASD more likely to face maltreatment, study finds
February 16, 2019 - Study finds genetic vulnerability to use of menthol cigarettes
February 16, 2019 - Promising drug developed to rejuvenate muscle cells
February 16, 2019 - H-RT should be the standard of care for men with low risk prostate cancer, study shows
February 16, 2019 - New technique using patients’ own modified cells could help treat Crohn’s disease
February 16, 2019 - Therapeutic endoscopy has an expanding role in the treatment of IBD
February 16, 2019 - Blood clot discovery could lead to development of better treatments for blood diseases
February 16, 2019 - Intervention can increase exclusive breastfeeding rates
February 16, 2019 - New project explores how gaming technologies can help cancer patients communicate better
February 16, 2019 - Catalyst Biosciences Presents Updated Data from Its Phase 2/3 Trial of Subcutaneous Marzeptacog Alfa (Activated) in Individuals with Hemophilia A or B with Inhibitors at the 12th Annual EAHAD Congress
February 16, 2019 - Rerouting nerves during amputation reduces phantom limb pain before it starts
February 16, 2019 - A Hormone Produced When We Exercise Might Help Fight Alzheimer’s
February 16, 2019 - Millions of British people breathe toxic air travelling to GPs
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