News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel

News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel
Sign In

Common DNA Testing Method Using SNP Chips Struggles to Find Rare Variants Associated with BRCA Test, UK Researchers Find

Results of the UK study confirm for clinical laboratory professionals the importance of fully understanding the design and function of SNP chips they may be using in their labs

Here is another example of a long-established clinical laboratory test that—upon new evidence—turns out to be not as accurate as once thought. According to research conducted at the University of Exeter in Devon, UK, Single-nucleotide polymorphism (SNP) chips (aka, SNP microarrays)—technology commonly used in commercial genetic testing—is inadequate at detecting rare gene variants that can increase breast cancer risk.  

A news release announcing the results of the large-scale study states, “A technology that is widely used by commercial genetic testing companies is ‘extremely unreliable’ in detecting very rare variants, meaning results suggesting individuals carry rare disease-causing genetic variants are usually wrong.”

Why is this a significant finding for clinical laboratories? Because medical laboratories performing genetic tests that use SNP chips should be aware that rare genetic variants—which are clinically relevant to a patient’s case—may not be detected and/or reported by the tests they are running.

UK Researchers Find ‘Shockingly High False Positives’

The objective of the Exeter study published in British Medical Journal (BMJ), titled, “Use of SNP Chips to Detect Rare Pathogenic Variants: Retrospective, Population Based Diagnostic Evaluation,” was “To determine whether the sensitivity and specificity of SNP chips are adequate for detecting rare pathogenic variants in a clinically unselected population.”

The conclusion reached by the Exeter researchers, the BMJ study states, is that “SNP chips are extremely unreliable for genotyping very rare pathogenic variants and should not be used to guide health decisions without validation.”  

Leigh Jackson, PhD, Lecturer in Genomic Medicine at University of Exeter and co-author of the BMJ study, said in the news release, “The number of false positives on rare genetic variants produced by SNP chips was shockingly high. To be clear: a very rare, disease-causing variant detected using [an] SNP chip is more likely to be wrong than right.” 

Caroline Wright, PhD, Professor in Genomic Medicine at the University of Exeter Medical School
In the news release, Caroline Wright, PhD (above), Professor in Genomic Medicine at the University of Exeter Medical School and senior author of the BMJ study, said, “SNP chips are fantastic at detecting common genetic variants, yet we have to recognize that tests that perform well in one scenario are not necessarily applicable to others.” She added, “We’ve confirmed that SNP chips are extremely poor at detecting very rare disease-causing genetic variants, often giving false positive results that can have profound clinical impact. These false results had been used to schedule invasive medical procedures that were both unnecessary and unwarranted.” (Photo copyright: University of Exeter.)

Large-Scale Study Taps UK Biobank Data

The Exeter researchers were concerned about cases of unnecessary invasive medical procedures being scheduled by women after learning of rare genetic variations in BRCA1 (breast cancer type 1) and BRCA2 (breast cancer 2) tests.

“The inherent technical limitation of SNP chips for correctly detecting rare genetic variants is further exacerbated when the variants themselves are linked to very rare diseases. As with any diagnostic test, the positive predictive value for low prevalence conditions will necessarily be low in most individuals. For pathogenic BRCA variants in the UK Biobank, the SNP chips had an extremely low positive predictive value (1-17%) when compared with sequencing. Were these results to be fed back to individuals, the clinical implications would be profound. Women with a positive BRCA result face a lifetime of additional screening and potentially prophylactic surgery that is unwarranted in the case of a false positive result,” they wrote.

Using UK Biobank data from 49,908 participants (55% were female), the researchers compared next-generation sequencing (NGS) to SNP chip genotyping. They found that SNP chips—which test genetic variation at hundreds-of-thousands of specific locations across the genome—performed well when compared to NGS for common variants, such as those related to type 2 diabetes and ancestry assessment, the study noted.

“Because SNP chips are such a widely used and high-performing assay for common genetic variants, we were also surprised that the differing performance of SNP chips for detecting rare variants was not well appreciated in the wider research or medical communities. Luckily, we had recently received both SNP chip and genome-wide DNA sequencing data on 50,000 individuals through the UK Biobank—a population cohort of adult volunteers from across the UK. This large dataset allowed us to systematically investigate the performance of SNP chips across millions of genetic variants with a wide range of frequencies, down to those present in fewer than 1 in 50,000 individuals,” wrote Wright and Associate Professor of Bioinformatics and Human Genetics at Exeter, Michael Weedon, PhD, in a BMJ blog post.

The Exeter researchers also analyzed data from a small group of people in the Personal Genome Project who had both SNP genotyping and sequencing information available. They focused their analysis on rare pathogenic variants in BRCA1 and BRCA2 genes.

The researchers found:

  • The rarer the variant, the less reliable the test result. For example, for “very rare variants” in less than one in 100,000 people, 84% found by SNP chips were false positives.
  • Low positive predictive values of about 16% for very rare variants in the UK Biobank.
  • Nearly all (20 of 21) customers of commercial genetic testing had at least one false positive rare disease-causing variant incorrectly genotyped.
  • SNP chips detect common genetic variants “extremely well.”

Advantages and Capabilities of SNP Chips

Compared to next-gen genetic sequencing, SNP chips are less costly. The chips use “grids of hundreds of thousands of beads that react to specific gene variants by glowing in different colors,” New Scientist explained.

Common variants of BRCA1 and BRCA2 can be found using SNP chips with 99% accuracy, New Scientist reported based on study data.

However, when the task is to find thousands of rare variants in BRCA1 and BRCA2 genes, SNP chips do not fare so well.

“It is just not the right technology for the job when it comes to rare variants. They’re excellent for the common variants that are present in lots of people. But the rarer the variant is, the less likely they are to be able to correctly detect it,” Wright told CNN.

SNP chips can’t detect all variants because they struggle to cluster needed data, the Exeter researchers explained.

“SNP chips perform poorly for genotyping rare genetic variants owing to their reliance on data clustering. Clustering data from multiple individuals with similar genotypes works very well when variants are common,” the researchers wrote. “Clustering becomes more difficult as the number of people with a particular genotype decreases.”

Clinical laboratories Using SNP Chips

The researchers at Exeter unveiled important information that pathologists and medical laboratory professionals will want to understand and monitor. Cancer patients with rare genetic variants may not be diagnosed accurately because SNP chips were not designed to identify specific genetic variants. Those patients may need additional testing to validate diagnoses and prevent harm.

—Donna Marie Pocius

Related Information:

Large-scale Study Finds Genetic Testing Technology Falsely Detects Very Rare Variants

Use of SNP Chips to Detect Rare Pathogenic Variants: Retrospective, Population-Based Diagnostic Evaluation

The Home DNA Kits “Falsely Warning of High Risk of Cancer”: DIY Genetic Tests are “Extremely Unreliable” at Detecting Rare Genetic Variants, Major New Study Warns

SNP Chips Perform Poorly for Detecting Rare Genetic Variants

Chip-based DNA Testing Wrong More than Right for Very Rare Variants

Common Genetic Tests Often Wrong When Identifying Rare Disease-Causing Variants Such as BRCA1and BRCA2, Study Says

Mayo Clinic Researchers Find Some Bacteria Derail Weight Loss, Suggest Analysis of Individuals’ Microbiomes; a Clinical Lab Test Could Help Millions Fight Obesity

CDC reports more than 93-million US adults are obese, and health issues related to obesity include heart disease, stroke, type 2 diabetes, and cancers

In recent years, the role of the human microbiome in weight loss or weight gain has been studied by different research groups. There is keen interest in this subject because of the high rates of obesity, and diagnostic companies know that development of a clinical laboratory test that could assess how an individual’s microbiome affects his/her weight would be a high-demand test.

This is true of a study published this year in Mayo Clinic Proceedings. Researchers at Mayo Clinic looked at obese patients who were in an active lifestyle intervention program designed to help them lose weight. It was determined that gut microbiota can have a role in both hindering weight loss and supporting weight loss.

Gut Microbiota More Complicated than Previously Thought

The Mayo researchers determined “an increased abundance of Phascolarctobacterium was associated with [successful weight loss]. In contrast, an increased abundance of Dialister and of genes encoding gut microbial carbohydrate-active enzymes was associated with failure to [lose] body weight. A gut microbiota with increased capability for carbohydrate metabolism appears to be associated with decreased weight loss in overweight and obese patients undergoing a lifestyle intervention program.”

How do bacteria impede weight loss? Vandana Nehra, MD, Mayo Clinic Gastroenterologist and co-senior author of the study, explained in a news  release.

“Gut bacteria have the capacity to break down complex food particles, which provides us with additional energy. And this is normally is good for us,” she says. “However, for some individuals trying to lose weight, this process may become a hindrance.”

Put another away: people who more effectively metabolized carbohydrates were the ones who struggled to drop the pounds, New Atlas pointed out.

Vandana Nehra, MD (left), and Purna Kashyap, MBBS (right), are Mayo Clinic Gastroenterologists and co-senior authors of the Mayo study. “While we need to replicate these findings in a bigger study, we now have an important direction to pursue in terms of potentially providing more individualized strategies for people who struggle with obesity,” Nehra noted in the news release. Thus, precision medicine therapy for obese individuals could be based on Mayo Clinic’s research. (Photo copyright: Mayo Clinic.)

Mayo Study Provides Clues to Microbiota Potential in Weight Loss

The Mayo researchers wanted to know how gut bacteria behave in people who are trying to lose weight.

They recruited 26 people, ranging in age from 18 to 65, from the Mayo Clinic Obesity Treatment Research Program. Fecal stool samples, for researchers’ analysis, were collected from participants at the start of the three-month study period and at the end.  The definition of successful weight loss was at least 5% of body weight.

Researchers found the following, according Live Science:

  • 2 lbs. lost, on average, among all participants;
  • Nine people were successful, losing an average of 17.4 lbs.;
  • 17 people did not meet the goal, losing on average just 3.3 lbs.; and,
  • More gut bacterial genes that break down carbohydrates were found in stool samples of the unsuccessful weight loss group, as compared to the successful dieters.

The researchers concluded that “An increased abundance of microbial genes encoding carbohydrate-active enzyme pathways and a decreased abundance of Phascolarctobacterium in the gut microbiota of obese and overweight individuals are associated with failure to lose at least 5% weight following a 3-month comprehensive lifestyle intervention program.”

Purna Kashyap, MBBS, Mayo Clinic Gastroenterologist and co-senior author of the study, told Live Science, “The study suggests there is a need to take the microbiome into account in clinical studies (on weight loss), and it also provides an important direction to pursue in terms of providing individualized care in obesity.” The very basis of precision medicine.

Future Weight-Loss Plans Based on Patient’s Microbiota

The Mayo Clinic researchers acknowledged the small sample size and need for more studies with larger samples over a longer time period. They also noted in their paper that Dialister has been associated with oral infections, such as gingivitis, and its role in energy expenditure and metabolism is unclear.

Still, the study suggests that it may soon be possible to give people individualized weight loss plans based on their gut bacteria. Clinical laboratory professionals and pathologists will want to stay abreast of follow-up studies and replication of findings by other research teams. A future medical laboratory test to analyze patients’ microbiomes could help obese people worldwide as well as lab business volume.

—Donna Marie Pocius

Related Information:

Gut Microbial Carbohydrate Metabolism Hinders Weight Loss in Overweight Adults Undergoing Lifestyle Intervention with a Volumetric Diet

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

CDC: Adult Obesity Facts

Makeup of an Individual’s Gut Bacteria May Play Role in Weight Loss, Mayo Study Suggests

Struggle to Lose Weight? Your gut Bacteria May Be to Blame

Your Gut Bacteria May Make It Harder to Lose Weight

Diet Hit a Snag? Your Gut Bacteria May be Partly to Blame

Can’t Lose Weight? Your Gut Bacteria Could be to Blame, According to Study

Richness of Human Gut Microbiome Correlates with Metabolic Markers

Annual Medical Spending Attributable to Obesity: Payer- and Service-Specific Estimates

5 Ways Gut Bacteria Affect Your Health

Cornell Researchers Identify Gut Microbes That May Help Some People Remain Thin; Findings Could Result in Clinical Laboratory Tests to Analyze Microbiomes of Individuals

Clinical Laboratories Might Soon be Diagnosing Obesity and Guiding Therapies that Utilize Engineered Microbes

Could ‘Money Back’ Guarantees Become More Common for Medical Devices, Clinical Laboratory Tests, and Prescription Drugs as Manufacturers Strive to Prove Clinical Value?

Examples already exist of manufacturers agreeing to refund payments if their therapeutic drugs don’t benefit patients; Medical laboratories with proprietary tests may find this strategy effective at guaranteeing the clinical utility of their assays

If their medical devices, medical laboratory tests, or prescription drugs are not effective, will payers, patients, and doctors get refunds from the manufacturers of these products? Some experts predict that the increased emphasis on improved patient outcomes, and the need for healthcare enterprises to back up the clinical value of their services, could lead to money-back guarantees and reimbursements for treatment therapies.

Offering a refund for services if the patient does not benefit is a powerful and compelling way for a company to call attention to its confidence level in its products and services.     (more…)

New Miniature Continuous Glucose Monitoring Devices from DexCom and Verily (Google Life Sciences) Promise to Make Glucose Monitoring Wearable and Affordable

Such a small, non-invasive glucose monitor would capture and transmit data to the Cloud, making it feasible for clinical laboratories to collect those tests results, and keep a record of each patient’s glucose results

Probably no single area of medical laboratory testing has the greatest potential to help the largest number of patients with a chronic disease—and make a lot of money for the in vitro (IVD) manufacturer who is first to market with the right diagnostic product—than glucose testing and continuous glucose monitoring (CGM). Pathologists and clinical laboratory managers know why this is true.

Reports from the Centers for Disease Control and Prevention (CDC) and the American Diabetes Association, state that more than 29 million Americans (about 9% of the U.S. population) have diabetes. Nearly 28% of these (about eight million) are undiagnosed. The reports also stipulate that fasting glucose or A1C levels have shown that more than 80 million people over the age of 20 were prediabetic in 2012. Based on trends since then, we can safely assume that the number of prediabetics in America has grown. And what is true in the United States is general true in most developed nations throughout the world. (more…)

Princeton Engineers Develop a Non-invasive Blood Glucose Test that Uses Imaging Technology

If validated in clinical trials, this novel technology has the potential to shift some glucose testing from the clinical laboratory by offering diabetics a convenient, painless blood sugar test

Glucose testing is both a headache and an opportunity for clinical laboratories here in the United States and across the globe. It is a headache because many point-of-care and patient self-test glucose devices in wide use today lack the reliability of glucose testing performed in medical laboratories that use sophisticated diagnostic instruments.

It is an opportunity because, here in the United States and across the globe, there are tens of millions of type 2 diabetics and hundreds of millions of pre-diabetics. Health systems have an unmet demand for glucose testing that is non-invasive, accurate, can be done in patient care settings, and is cheap.

Recently, researchers at Princeton University announced development of noninvasive, in vivo glucose sensor technology that uses a broad-spectrum band of infrared (IR) light to accurately measure blood sugar.

The clinical market for such a device is huge. Just in the United States, there are more than 30 million diagnosed with type 2 diabetes, and more than 70 million pre-diabetics. Researchers have been working for some time to develop a patient-friendly glucose-monitoring technology that does not require a needle stick or venipuncture. (more…)

;