Breaking News
April 19, 2019 - Key research takeaways from ECCMID 2019
April 19, 2019 - AI Can Identify Model of Cardiac Rhythm Device From Chest X-Ray
April 19, 2019 - New way to combat childhood anxiety: treat the parents
April 19, 2019 - Women getting C-sections best judge of own pain medication needs | News Center
April 19, 2019 - Immune responses that prevent fungal infections may eliminate Trichinella spiralis
April 19, 2019 - Exercising in the morning, rather than at night, may yield better results, shows study
April 19, 2019 - Why eating ‘right’ could cause you to stray from your diet
April 19, 2019 - Health Tip: Antidepressant Precautions – Drugs.com MedNews
April 19, 2019 - Bigger portions lead to preschoolers eating more over time
April 19, 2019 - Specific strains of Staphylococcus aureus linked to wounds that do not heal
April 19, 2019 - Revolutionary discovery paves new way for treatment of necrotizing enterocolitis
April 19, 2019 - Drug that treats high blood pressure shows promise against neurodegenerative diseases
April 19, 2019 - More care is needed for patients after kidney transplantations, reports research
April 19, 2019 - Virtual reality offers benefits for Parkinson’s disease patients
April 19, 2019 - Liver Illness Strikes Latino Children Like A ‘Silent Tsunami’
April 19, 2019 - Disruptive behaviors in autistic children linked to reduced brain connectivity
April 19, 2019 - New insights into how vitamin D affects immune system
April 19, 2019 - Pfizer Announces Presentation of Data from a Phase 2 Study of its 20-Valent Pneumococcal Conjugate Vaccine Candidate Being Investigated for the Prevention of Invasive Disease and Pneumonia in Adults Aged 18 Years and Older
April 19, 2019 - Exercise can improve non-motor symptoms of Parkinson’s disease
April 19, 2019 - KZFPs play a key role in the regulation of human genome
April 19, 2019 - Extracts of ginkgo seeds show antibacterial activity on pathogens that cause skin infections
April 19, 2019 - Groundbreaking experiment in pigs challenges the notion about brain damage
April 19, 2019 - Improving the quality of digital pathology imaging
April 19, 2019 - Scientists get closer to injecting artificial lymph nodes into people to fight disease
April 19, 2019 - Exercises and swimming goggles may reduce adverse effects on eye during long spaceflights
April 19, 2019 - Review suggests a reciprocal relationship between obesity and self-control
April 19, 2019 - Study identifies how enterococci bacteria cause antibiotic-resistant bloodstream infections
April 19, 2019 - Triple negative breast cancer develop resistance to chemotherapy by turning on molecular pathway
April 19, 2019 - Researchers identify key clues to brain and pancreas development
April 19, 2019 - Metformin May Cut Risk for Prematurity, Miscarriage in PCOS
April 19, 2019 - Obese mouse mothers trigger heart problems in offspring
April 19, 2019 - Research sheds light on how leukemia cells become resistant to drugs
April 19, 2019 - Health Tip: Stopping Nosebleeds – Drugs.com MedNews
April 19, 2019 - Pediatric endocrinologist gives iconic ‘Mona Lisa’ a second medical opinion
April 19, 2019 - Tapping patients’ wisdom for C-section pain management
April 18, 2019 - Why have autism rates ‘exploded’ in New Jersey?
April 18, 2019 - Microbiome science may help doctors to improve treatment for children with IBS
April 18, 2019 - New gene therapy cures babies with fatal ‘Bubble Boy’ disease
April 18, 2019 - No female mice? Scientists may still approve NIH grant
April 18, 2019 - What needs to be said about mental health in medicine
April 18, 2019 - Hickenlooper Expanded Medicaid, Created State-Run Marketplace To Insure Nearly All Coloradans
April 18, 2019 - Cancer cells grown in tumor-mimicking environment can help predict the effect of experimental drugs
April 18, 2019 - Albireo Announces FDA Clearance of IND to Commence Phase 2 Trial of Elobixibat for the Treatment of NAFLD/NASH
April 18, 2019 - Adhesive gel bonds to eye surface, could repair injuries without surgery
April 18, 2019 - The future of genomics: A podcast featuring Stanford geneticists
April 18, 2019 - As Syphilis Invades Rural America, A Fraying Health Safety Net Is Failing To Stop It
April 18, 2019 - APOE gene impacts sleep depending on gender and severity of Alzheimer’s
April 18, 2019 - PCORI’s newly approved awards focus on cancer pain and opioid use disorders
April 18, 2019 - New tool provides a standard way to measure effects of caring for survivors of TBI
April 18, 2019 - Smartphone use risks eye examination misdiagnosis
April 18, 2019 - How drug-resistant bugs grow in CF patients’ lungs
April 18, 2019 - Gordana Vunjak-Novakovic Elected to American Academy of Arts & Sciences
April 18, 2019 - Podcast: KHN’s ‘What The Health?’ You Have Questions, We Have Answers
April 18, 2019 - Diabetic drug shows potential to be repurposed as heart disease treatment for non-diabetic patients
April 18, 2019 - New estimation method assesses natural variations in sex ratio at birth
April 18, 2019 - UTA scientist receives $1.17 million grant for cancer research
April 18, 2019 - Coagulation factor VIIa prevents bleeds in hemophilia animal models
April 18, 2019 - Researchers identify risk factors for severe infection after knee replacement
April 18, 2019 - Mass drug administration can offer community-level protection against malaria
April 18, 2019 - FDA’s added sugar label could have substantial health and cost-saving benefits
April 18, 2019 - Researchers identify cause of inherited metabolic disorder
April 18, 2019 - Single strip of white paint not sufficient to protect people who ride bikes
April 18, 2019 - Partner status influences link between sexual problems and self-efficacy in breast cancer survivors
April 18, 2019 - Colorectal Neoplasia Risk Up for Hodgkin Lymphoma Survivors
April 18, 2019 - Rigid spine muscular dystrophy – Genetics Home Reference
April 18, 2019 - Simple bile acid blood test could tell risk of stillbirth
April 18, 2019 - Center for Experimental Therapeutics aims to enable all steps of drug development | News Center
April 18, 2019 - Falling for telephone scams could be an early sign of dementia
April 18, 2019 - Researchers annotate key neuronal proteins in lamprey genome
April 18, 2019 - Study uncovers new biomarker for personalized cancer treatments
April 18, 2019 - Scientists enter research collaboration to find a cure for cancer
April 18, 2019 - Study to compare benefits of tai chi and mindfulness meditation on MS symptoms
April 18, 2019 - Gestational diabetes during pregnancy may increase risk of type 1 diabetes in children
April 18, 2019 - Maternal age has no effect on IVF success, conclude researchers
April 18, 2019 - Is a New Remedy for Body Odor on the Horizon?
April 18, 2019 - Orthostatic hypotension – Genetics Home Reference
April 18, 2019 - Healing the heartbreak of stillbirth and newborn death
April 18, 2019 - New study calls healthiness of eggs into question
April 18, 2019 - Conference to highlight advances in human immune monitoring, bioinformatics | News Center
April 18, 2019 - Bacteria use viruses for self-recognition, study reveals
New algorithm could accelerate diagnosis of genetic diseases using clinical records

New algorithm could accelerate diagnosis of genetic diseases using clinical records

image_pdfDownload PDFimage_print

In a continued effort to speed up the diagnostic process of severe genetic diseases, Stanford’s Gill Bejerano, PhD, and his colleagues have developed a new algorithm that can quickly locate important disease-related information within a patient’s medical record.

In a paper recently published in Nature Genetics in Medicine, Bejerano and Cole Deisseroth, a Bio-X undergraduate fellow, along with researchers including Johannes Birgmeier, a graduate student in computer science, developed an algorithm that scans through records of patients and extracts the patient’s key phenotypes, or observable traits.

The team focused particularly on patients with life-threatening genetic diseases such as sickle cell anemia, cystic fibrosis and Huntington’s disease. Manually scanning through patient notes without a computer, a dedicated clinician can process around 200 patient records in a 40-hour work week, the researchers said. This algorithm can do the same job in 10 minutes, further saving busy doctors an additional three to five hours per every downstream disease diagnosis.

“A diagnosis is extremely valuable for the patient, for the family and for the attending clinician,” said Bejerano. But finding the diagnosis within the patient’s genome is very time consuming and, “for that we need computational tools.”

The algorithm is called ClinPhen — a combination of “clinical” and “phenotypes.” After examining a patient’s medical records, the algorithm parses the sentences into short phrases. For example, if the clinical note reads, “The child has short stature and long eyelashes. She has a cleft palate and a small jaw,” the phrases, “The child has short stature”, “and long eyelashes”, “She has a cleft palate”, and “a small jaw” would be selected.

These phrases are converted into codes from an existing phenotype database called the Human Phenotype Ontology, or HPO. The codes are then sorted, with the most- and earliest-mentioned phenotypes at the top of the list. ClinPhen can also identify words, such as “father” and “does not have” and not associate any phenotypes mentioned in that sentence with the patient.

ClinPhen’s accuracy, phenotype filter and speed was validated using six sets of real patient clinical notes from four different medical centers. When compared to other phenotype extraction algorithms, ClinPhen was more precise and 20 times faster, the research showed.

“ClinPhen actually guesses slightly better than a clinician,” Bejerano said. “We can capture clinician intuition and pick the right set of phenotypes to best facilitate the diagnosis.”

The HPO codes produced by ClinPhen will then be fed to Phrank, another algorithm designed by Bejerano and his colleagues that ranks patients’ genes that have rare variants for their ability to explain the phenotypes, or traits, identified by ClinPhen.

Bejerano describes the efforts as a “computational ecosystem”, and said he hopes to see this ecosystem implemented in clinical settings soon.

“The medical establishment is very conservative. And for good reason… You want to protect the patient,” Bejerano said. “[But] I think that slowly, very slowly, there is a shift towards using more of these automated systems. With 60 million patients to be sequenced in the next several years, we simply have no choice.”

Image by Darryl Leja, NHGRI

Tagged with:

About author

Related Articles