Nov 9, 2018 | Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Pathology
Studies show consumer genealogy databases are much broader than is generally known. If your cousins are in such a database, it’s likely you are too
Recent news stories highlighted crime investigators who used the DNA data in consumer genetic genealogy databases to solve cold cases. Though not widely known, such uses of direct-to-consumer DNA databases is becoming more commonplace, which might eventually lead to requests for clinical laboratories to assist in criminal investigations involving DNA data.
Case in point: investigators found the Golden State Killer, a serial killer/rapist/burglar who terrorized multiple California counties over a dozen years in the 1970s to 1980s, after uploading a DNA sample from the crime scene to GEDmatch, an open-data genomics database that features tools for genealogy research. They made the arrest after discovering a distant relative’s DNA in the genealogy database and matching it to the suspect, CBS News revealed in a 60 Minutes Overtime online report.
These and other investigators are using a technique called familial DNA testing (AKA, DNA Profiling), which enables them to use genetic material from relatives to solve crimes.
Clinical laboratories oversee DNA databases. Could DNA databases—developed and managed over years by medical laboratories for patient care—be subpoenaed by law enforcement investigating crimes?
The question raises many issues for society and for labs, including privacy responsibilities and appropriate use of genetic information. On the other hand, the genetic genie is already out of the bottle.
Leveraging Familia DNA to Solve Crimes a New Trend
“The solving of the Golden State Killer case opened this method up as a possibility, and other crime labs are taking advantage of it. Clearly, a trend has started,” Ruth Dickover, PhD, Director of Forensic Science, University of California, Davis, told the Los Angeles Times.
Indeed, the use of familial DNA testing is moving forward. The Verge reported 19 cold case samples have been identified in recent familial DNA testing and public database searches. It also said two new published studies may propel the technique further.
One study, published in the journal Science, suggests nearly every American of European ancestry may soon be identified through familial DNA testing.
The other study, published in Cell, shows that a person’s relatives can be detected when forensic DNA data are compared with consumer genetic databases.
Noah Rosenberg, PhD (above left), Professor of Population Genetics and Society Biology at Stanford University, is shown above working with Jaehee Kim, PhD (right), a Postdoctoral Research Fellow in Biology, on math that could be used to track down relatives in genealogy databases based on forensic DNA. “This could be a way of expanding the reach of forensic genetics, potentially for solving even more cold cases. But at the same time, it could be exposing participants in those databases to forensic searches they might not have anticipated,” he told Wired. (Photo copyright: Stanford University/L.A. Cicero.)
15 Million People Already in Genealogy Databases
Researchers at Columbia University in New York and Hebrew University of Jerusalem told Science they were motivated by the recent trend of investigations leveraging third-party consumer genomics services to find criminals. But they perceived a gap.
“The big limitation is coverage. And even if you find an individual it requires complex analysis from that point,” Yaniv Erlich, PhD, Associate Professor at Columbia and Chief Science Officer at MyHeritage, told The Verge. MyHeritage is an online genealogy platform.
Others offering consumer genetic testing and family history exploration include 23andMe and Ancestry. As of April 2018, more than 15 million people have participated in direct-to-consumer genetic testing, the researchers noted.
The study aimed to find the likelihood that a person can be identified using a long-range familial search. It included these steps and findings:
- Statistical analysis of 1.28 million people in the MyHeritage database;
- Pairs of people with “identity-by-descent” were removed to avoid bias, such as first cousins and closer relationships;
- Researchers aimed at finding a third cousin or closer relatives for each person in the database;
- 60% of the 1.28 million people were matched with a third cousin or closer relative.
“We project that about 60% of the searches for individuals of European-descent will result in a third cousin or closer match, which can allow their identification using demographic identifiers. Moreover, the technique could implicate nearly any US individual of European descent in the near future,” the researchers wrote.
In an interview with Wired, Erlich added, “The takeaway is it doesn’t matter if you’ve been tested or not tested. You can be identified because the databases already cover such large fractions of the US—at least for European ancestry.”
Matching Forensic and Consumer Genetic Data
Meanwhile, the study published in Cell by researchers at Stanford University, University of California, Davis, and the University of Michigan also suggests investigators could compare forensic DNA samples with consumer genetic databases to find people related to criminals.
That study found:
- 30% to 32% of people in a forensic database could be related to a child or parent in a consumer database;
- 35% to 36% could be tied to a sibling.
These studies reveal that genetic data and familial DNA testing can help law enforcement find suspects, which is a good thing for society. But people who uploaded DNA data to some direct-to-consumer databases may find themselves caught up in searches they do not know about. So may their cousins.
Dark Daily recently covered other similar studies that showed it takes just one person’s DNA to reveal genetic information on an entire family. (See, “The Problems with Ancestry DNA Analyses,” October 18, 2018.) These developments in the use of DNA databases to identify criminals should be an early warning to clinical laboratories building databases of genetic information that, at some future point, law enforcement agencies might want access to those databases as part of ongoing criminal investigations.
—Donna Marie Pocius
Related Information:
Could Your DNA Help Solve a Cold Case?
So Many People Have Had Their DNA Sequenced That They’ve Put Other People’s Privacy in Jeopardy
The DNA Technique That Caught the Golden State Killer is More Powerful than We Thought
Identity Inference of Genomic Data Using Long-Range Familial Searches
Statistical Detection of Relatives Typed with Disjoint Forensic and Biomedical Loci
Genome Hackers Show No One’s DNA is Anonymous Anymore
Stanford Researchers Discover a New Way to Find Relatives from Forensic DNA
The Problems with Ancestry DNA Analyses
Nov 7, 2018 | Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory News, Laboratory Pathology, Laboratory Testing, Management & Operations
CRISPR-Cas9 connection to cancer prompts research to investigate different approaches to gene editing
Dark Daily has covered CRISPR-Cas9 many times in previous e-briefings. Since its discovery, CRISPR, or Clustered Regularly Interspaced Short Palindromic Repeats, has been at the root of astonishing breakthroughs in genetic research. It appears to fulfill precision medicine goals for patients with conditions caused by genetic mutations and has anatomic pathologists, along with the entire scientific world, abuzz with the possibilities such a tool could bring to diagnostic medicine.
All of this research has contributed to a deeper understanding of how cells function. However, as is often the case with new technologies, unforeseen and problematic questions also have arisen.
CRISPR-Cas9 Connection to Cancer
Research conducted at the Wellcome Sanger Institute in the United Kingdom (UK) and published in Nature Biotechnology, examined potential damage caused by CRISPR-Cas9 editing.
“Here we report significant on-target mutagenesis, such as large deletions and more complex genomic rearrangements at the targeted sites in mouse embryonic stem cells, mouse hematopoietic progenitors, and a human differentiated cell line,” wrote the authors in their introduction.
Another study, this one conducted by biomedical researches at Cambridge, Mass., and published in Nature, describes possible toxicity caused by Cas9.
“Our results indicate that Cas9 toxicity creates an obstacle to the high-throughput use of CRISPR-Cas9 for genome engineering and screening in hPSCs [human pluripotent stem cells]. Moreover, as hPSCs can acquire P53 mutations, cell replacement therapies using CRISPR-Cas9-enginereed hPSCs should proceed with caution, and such engineered hPSCs should be monitored for P53 function.”
Essentially what both groups of researchers found is that CRISPR-Cas9 cuts through the double helix of DNA, which the cell responds to as it would any injury. A gene called p53 then directs a cellular “first-aid kit” to the “injury” site that either initiates self-destruction of the cell or repairs the DNA.
Therefore, in some instances, CRISPR-Cas9 is inefficient because the repaired cells continue to function. And, the repair process involves the p53 gene. P53 mutations have been implicated in ovarian, colorectal, lung, pancreatic, stomach, liver, and breast cancers.
Though important, some experts are downplaying the significance of the findings.
Erik Sontheimer, PhD (above), Professor, RNA Therapeutics Institute, at the University of Massachusetts Medical School, told Scientific American that the two studies are important, but not show-stoppers. “This is something that bears paying attention to, but I don’t think it’s a deal-breaker,” he said. (Photo copyright: University of Massachusetts.)
“It’s something we need to pay attention to, especially as CRISPR expands to more diseases. We need to do the work and make sure edited cells returned to patients don’t become cancerous,” Sam Kulkarni, PhD, CEO of CRISPR Therapeutics, told Scientific American.
Both studies are preliminary. The implications, however, is in how genes that have become corrupted are used.
“It is unclear if the findings translate into cells actually used in clinical studies,” Bernhard Schmierer, PhD, co-author of a paper titled, “CRISPR-Cas9 Genome Editing Induces a p53-mediated DNA Damage Response,” told Scientific American.
Nevertheless, the cancer-cat is out of the bag.
Targeting RNA Instead of DNA with CRISPR-Cas13d
A team from the Salk Institute may have found a solution. They are investigating a different enzyme—Cas13d—which, in conjunction with CRISPR would target RNA rather than DNA. “DNA is constant, but what’s always changing are the RNA messages that are copied from the DNA. Being able to modulate those messages by directly controlling the RNA has important implications for influencing a cell’s fate,” Silvana Konermann, PhD, a Howard Hughes Medical Institute (HHMI) Hanna Gray Fellow and member of the research team at Salk, said in a news release.
The Salk team published their findings in the journal Cell. The paper describes how “scientists from the Salk Institute are reporting for the first time the detailed molecular structure of CRISPR-Cas13d, a promising enzyme for emerging RNA-editing technology. They were able to visualize the enzyme thanks to cryo-electron microscopy (cryo-EM), a cutting-edge technology that enables researchers to capture the structure of complex molecules in unprecedented detail.”
The researchers think that CRISPR-Cas13d may be a way to make the process of gene editing more effective and allow for new strategies to emerge. Much like how CRISPR-Cas9 led to research into recording a cell’s history and to tools like SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing), a new diagnostic tool that works with CRISPR and changed clinical laboratory diagnostics in a foundational way.
Dark Daily reported on this breakthrough last year. (See, “CRISPR-Related Tool Set to Fundamentally Change Clinical Laboratory Diagnostics, Especially in Rural and Remote Locations,” August 4, 2017.)
Each discovery will lead to more branches of inquiry and, hopefully, someday it will be possible to cure conditions like sickle cell anemia, dementia, and cystic fibrosis. Given the high expectations that CRISPR and related technologies can eventually be used to treat patients, pathologists and medical laboratory professionals will want to stay informed about future developments.
—Dava Stewart
Related Information:
Repair of Double-Strand Breaks Induced by CRISPR-Cas9 Leads to Large Deletions and Complex Rearrangements
P53 Inhibits CRISPR-Cas9 Engineering in Human Pluripotent Stem Cells
CRISPR-Edited Cells Linked to Cancer Risk in 2 Studies
CRISPR-Cas9 Genome Editing Induces a p53-Mediated DNA Damage Response
Decoding the Structure of an RNA-Based CRISPR System
Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d
CRISPR Timeline
What Are Genome Editing and CRISPR-Cas9?
Federal Court Sides with Broad in CRISPR Patent Dispute
Top Biologists Call for Moratorium on Use of CRISPR Gene Editing Tool for Clinical Purposes Because of Concerns about Unresolved Ethical Issues
CRISPR-Related Tool Set to Fundamentally Change Clinical Laboratory Diagnostics, Especially in Rural and Remote Locations
Researchers at Several Top Universities Unveil CRISPR-Based Diagnostics That Show Great Promise for Clinical Laboratories
Mar 16, 2017 | Instruments & Equipment, Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
Every medical laboratory ready to begin the move away from fee-for-service payment and towards value-based reimbursement needs to start offering lab tests that support the practice of precision medicine
Nearly every clinical laboratory and pathology group in America today is aware of the opportunity to provide medical laboratory tests that enable physicians to successfully practice precision medicine. The goal of precision medicine is to enable a patient to get a more accurate diagnosis, receive the most appropriate therapy, and have his/her condition monitored with unprecedented insight during the course of treatment.
The good news for the clinical laboratory industry concerning precision medicine is that it is the fastest-growing sector of lab testing and these are the tests that contribute the greatest value in patient care. For example, molecular and genetic tests are revolutionizing the diagnosis and treatment of infectious disease. These are the clinical lab tests that enable a physician to identify the specific subtype of the bacteria or virus, then help him or her select the therapeutic drug that will have maximum benefit for the patient.
Clinical Laboratories Support Cancer Diagnosis with Companion Diagnostic Tests
It is equally true that the diagnosis and treatment of cancer is undergoing a major transformation. Genetic knowledge is being used to develop both diagnostic tests and new therapies that enable physicians to better diagnose cancer, and then treat it with the drugs identified by a companion diagnostic test as having the best potential to cure the patient or slow the progression of the disease.
But if there is an area of precision medicine with immense potential, it is pharmacogenomics and its associated testing.
In 2015, the Kaiser Family Foundation reported that more than four billion prescriptions were filled in the United States. As science understands more about the human genome, proteome, metabolome, and microbiome (to name just a few of the “omes”), it becomes possible to design clinical laboratory tests that:
1. Contribute to a more accurate diagnosis;
2. Identify which prescription drugs will be of the greatest benefit; and
3. Inform the physician as to which drugs will not be effective and may even be harmful to the patient.
More Good News for Medical Laboratories
There is even more good news. Many clinical laboratories, hospital labs, and pathology groups already have lab instruments capable of performing the tests used in precision medicine. For these labs, no major up-front investment is needed to begin offering tests that allow physicians to practice precision medicine.
“Many of our lab clients got started in this way,” stated Don Rule, MBA, Founder and Chief Executive Officer of Translational Software in Bellevue, Wash. “They realized that their existing lab instruments could run some of the lab tests physicians use when practicing precision medicine. This would be a low-cost way to enter the precision medicine field and they could, on a small scale with minimal risk, begin offering these tests to gain experience, learn more about the market, and identify which such tests would have highest value to the physicians in the communities they serve.”
Is Your Pathology Group Interested in Supporting Precision Medicine?
“For a lab that is serious about understanding the current and future clinical demand for precision medicine tests, several careful steps are recommended,” he continued. “One step is to build demand by educating clinicians and their staffs about the best ways to use these tests to improve patient care. Keep in mind that more of a physician’s reimbursement is now keyed to the patient outcomes they deliver. These doctors recognize that labs helping them do a better job with precision medicine are also helping them demonstrate greater value in the patient care they provide.
“There are other steps required to launch an effective, clinically successful precision medicine testing program,” Rule noted. “For example, labs need to understand how to be paid by the health insurers in their region. That includes getting in-network and teaching physicians and lab staff how to follow each payer’s clinical and coding criteria so that clean claims will be paid in a timely manner.
“Another step is to build the market in a careful fashion,” he emphasized. “For example, labs should identify the thought leaders among their clients and work with them to demonstrate the clinical utility of tests performed in support of precision medicine. And above all, it’s important to focus on patients that are most likely to get some insight from testing. When your lab starts with the right population, it’s remarkable how often you will uncover actionable issues.”
Clinical Labs Can Enter Precision Medicine by Initially Referring Tests
“It’s also feasible for a lab to start its precision medicine strategy by referring out testing in the early stages and using third-party experts to do the interpretations,” Rule advised. “Then, as specimen volume increases, and the lab’s clinical team gains more experience with these molecular and genetic tests, it becomes easy to bring that testing in-house to develop the market further with faster turnaround times and in-house expertise that local physicians appreciate.”
Every clinical lab, hospital lab, and pathology group that is considering how to support precision medicine will want to participate in a special webinar, titled, “What Molecular and Genetic Testing Labs Need to Know to Succeed with Commercialization of Their Precision Medicine Products.” It will take place on Wednesday, March 22, 2017 at 1 PM EDT.
Two expert speakers will cover the essentials that all labs should know about building a market presence in precision medicine. First to present is Don Rule of Translational Software. Rule currently provides a variety of services to more than 80 lab clients, which includes the annotation and interpretation of gene sequences. In addition, Rule and his team provide consulting expertise to help labs develop their strategies for precision medicine, identify the best tests to offer physicians, and develop the steps needed to obtain network status with payers.
Webinar Will Present the Best Successes of Molecular, Genetic Testing Labs
Rule will share the experiences and best successes of the molecular and genetic testing labs he has worked with since 2009. He will discuss the types of lab tests used in precision medicine in different specialties, identify the fastest-growing sectors, and note which instruments already found in most clinical laboratories can be used to provide lab tests used for precision medicine.
Don Rule (above left), Founder and CEO of Translational Software, and Kyle Fetter (above right), Vice President of Advanced Diagnostics at XIFIN, will share their unique insights, knowledge, and experience at developing a precision medicine lab testing program for clinical laboratories that want to build more market share, make the billing/collections team more effective, and increase revenue. (Photo copyright: Dark Daily.)
As one example, a growing number of long-term care facilities are using tests to practice precision medicine—and paying for these tests under value-based arrangements—because so many of their patients are taking from 10 to 15 prescriptions each day. If a lab test indicates that the patient may not be getting therapeutic benefit from a specific drug (or that there are negative side effects from the polypharmacy), then the long-term care facility is money ahead because of less spending on drugs and the decreased care costs from patients who remain healthier. In the extreme case, the care facility might lose a patient to a skilled nursing facility due to mental fog or a fall that is precipitated by adverse drug effects.
Making the Case for a Precision Medicine Lab Testing Program
Additional topics to be discussed are:
• How to make the case to administration and the clinicians;
• How to build demand; and
• How to identify thought leaders and work with them to educate the physicians in the lab’s service region.
The second speaker will address the important topic of how to get paid. Kyle Fetter, MBA, is Vice President of Advanced Diagnostics at XIFIN, Inc., based in San Diego. XIFIN provides revenue cycle management (RCM) services to more than 200 labs and handles as many as 300 million lab test claims annually. What this means is that Fetter sees which labs are most successful with their coding, billing, and collections for molecular and genetic tests. He also sees how different payers are handling these claims.
During his presentation, Fetter will provide you and your lab team with valuable knowledge about the best ways to collect the information needed to submit clean claims and be paid promptly. He will illustrate ways to optimize the process of gathering this data and the different software tools that not only make the job easier, but help ensure that a higher proportion of claims are clean and paid at first submission.
Secrets of Preparing for Payer Challenges, Denials, and Audits
But the single best element of Fetter’s presentation will be how labs performing molecular and genetic testing should prepare, as part of the normal course of business, for the inevitable challenges, denials, and audits. He will describe the elements of a system that helps labs be ready to make the case that claims are properly documented, and that they represent appropriate and necessary tests for the patient.
You can find details for this important webinar at this link. (Or copy this URL and paste it into your browser: https://www.darkdaily.com/webinar/what-molecular-and-genetic-testing-labs-need-to-know-to-succeed-with-commercialization-of-their-precision-medicine-products.)
This webinar is perfect for any lab that is already performing molecular and genetic tests, and which is interested in building more market share, making the billing/collections team more effective, and increasing revenue.
For every lab watching the precision medicine space, this webinar is a “must attend” because it delivers to you and your lab team the collective knowledge and insights from two experts who are working with hundreds of the nation’s most successful labs. It is your guaranteed way to get the accurate, relevant information you need to craft your own lab’s strategy for expanding its molecular and genetic testing opportunities.
—Michael McBride
Related Information:
Genetic Tests and Precision Medicine Start to Win Acceptance by Some Payers; Pathologists and Clinical Laboratories Have Opportunity as Advisors
Jan 4, 2017 | Laboratory Instruments & Laboratory Equipment, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing
Researchers believe they have begun to crack open a ‘black box’ involving the genomes and diseases of individual patients
Researchers in Switzerland are developing a new way to use mass spectrometry to explain why patients respond differently to specific therapies. The method potentially could become a useful tool for clinical laboratories that want to support the practice of precision medicine.
It is also one more example of how mass spectrometry is being used by researchers to develop new types of diagnostic assays that perform as well as traditional clinical laboratory testing methods, such as chemistry and immunoassay.
Thus, the latest research from the Swiss Federal Institute of Technology in Lausanne (EPFL) and ETH Zurich (ETHZ), will be of interest to pathology laboratory managers and medical laboratory scientists. It combines SWATH-MS (Sequential Window Acquisition of all Theoretical Mass Spectra) with genomics, transcriptomics, and other “omics,” to explain why patients respond differently to specific therapies, and to formulate a personalized strategy for individual treatment. (more…)
Jul 15, 2016 | Coding, Billing, and Collections, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
Most insurers still determine coverage on a case-by-case basis, but two major payers now have coverage policies that are helpful to clinical labs that perform WES
Whole exome sequencing (WES) is not new for clinical pathologists, but it is becoming more common in a clinical setting as more physicians learn about its uses.
This is due to two reasons. First, researchers are identifying new ways to use whole exome sequencing to improve patient care. Second, the cost of whole genome sequencing continues to fall at a steady rate, making it ever more affordable to use in clinical settings.
As recently as 2009, WES was prohibitively expensive and there was little possibility that insurers would cover the cost of the test, as it was considered experimental. Now, however, evidence is mounting that it is an effective diagnostic tool. Therefore, more payers are announcing coverage for WES for an expanding number of diagnostic purposes. (more…)
