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News Article | April 17, 2017
Site: www.eurekalert.org

A recent survey of over 2,000 women newly diagnosed with breast cancer found that half of those who undergo bilateral mastectomy after genetic testing don't actually have mutations known to confer increased risk of additional cancers, according to a study by researchers at the Stanford University School of Medicine and four other U.S. medical centers. Instead the women had what are known as variants of uncertain significance, or VUS, that are often eventually found to be harmless. A bilateral mastectomy is a surgical procedure in which both of a woman's breasts are removed after a diagnosis of cancer in one breast. The finding highlights the need for genetic counselors to help both patients and physicians better understand the results of genetic testing intended to determine a woman's risk for cancer recurrence or for developing a separate cancer in her ovaries or unaffected breast. "Our findings suggest a limited understanding among physicians and patients of the meaning of genetic testing results," said Allison Kurian, MD, associate professor of medicine and of health research and policy at Stanford. "Clinical practice guidelines state that variants of uncertain significance should not be considered to confer high cancer risk, and that patients with these variants should be counseled similarly to a patient whose genetic test is normal. However, many of the physicians surveyed in our study stated that they manage these patients in the same way as they do patients with mutations known to increase a woman's risk." Only about half of the surveyed women who received genetic testing ever discussed their test results with a genetic counselor, and between one-quarter and one-half of the surveyed breast cancer surgeons indicated they treat women with VUS no differently than women with known cancer-associated mutations, the researchers found. Furthermore, some women undergo surgery prior to receiving genetic testing or seeing the results. Kurian is the lead author of the study, which will be published online April 12 in the Journal of Clinical Oncology. University of Michigan researchers Reshma Jagsi, MD, DPhil, and Steven Katz, MD, MPH, share senior authorship. The findings come on the heels of a February study by many of the same researchers showing that physicians often fail to recommend genetic testing for breast cancer patients at high risk for mutations in the BRCA1 or BRCA2 genes, which are strongly associated with ovarian and other cancers. In this study, the researchers asked 2,502 women newly diagnosed with breast cancer whether they had received genetic testing, and if so, whether the testing and any discussion of results occurred before or after breast surgery. They found that of the 666 women who had received testing, 59 percent were considered to have a high risk of a dangerous mutation in a cancer-associated gene. About one-quarter of these women had genetic testing only after surgery -- meaning critical decisions were made about their care before information about their mutation status was available. Delays in testing were particularly pronounced in women who lacked private health insurance. The researchers then polled the surgeons who treated the women in the survey. They found that, when compared with doctors who had treated 51 or more newly diagnosed breast cancer patients during the previous year, doctors who had treated fewer than 21 breast cancer patients were: less confident in discussing the results of genetic testing with patients, more likely to order the genetic test without referring women to a genetic counselor, less likely to delay surgery in order to have test results available for surgical decision-making and more likely to manage a patient with variants of uncertain significance in the same way they would manage patients with proven high-risk mutations in cancer-associated genes. "Our findings suggest that we are not maximizing the benefit of genetic testing for our patients with breast cancer because of barriers related to timeliness of testing and lack of expertise necessary to incorporate results into treatment decisions," said Katz, who is a professor of medicine and of health management and policy at the University of Michigan. Although genetic testing has become more common and less costly, it's also become more confusing. The advent of multiplex gene panels that simultaneously test for mutations or variations in many different genes can render results that are difficult to interpret without the help of a trained genetic counselor. Uncertainties as to the meaning of test results may lead less-experienced surgeons to recommend aggressive treatment in the form of bilateral mastectomies, or cause women to opt for what they may feel is the safest option to manage their cancer. Conversely, high-risk women who do carry dangerous mutations need this information to make informed decisions about their health care choices. "The gaps identified in this study are striking," said Jagsi, professor and deputy chair of radiation oncology at the University of Michigan. "It is critical to ensure that patients at high risk for known cancer-associated mutations are fully informed of the potential benefits of genetic testing, and counseled accurately about the meaning of test results." "We're learning that clinicians' knowledge of breast cancer genetics can be highly variable," said Kurian, who is a member of the Stanford Cancer Institute. "It's important for women at high risk of carrying a dangerous mutation to see someone with expertise in cancer genetics when planning their care. Unfortunately, in many cases genetic counselors may not be optimally integrated into the care of newly diagnosed cancer patients, making it difficult to rapidly triage these patients. Our study highlights the urgent need for improved patient access to cancer genetics experts, particularly genetic counselors, and for educating physicians about the appropriate use of genetic testing and interpretation of test results." Researchers from the University of Southern California, Emory University and the Memorial Sloan-Kettering Cancer Center also contributed to the study. The study was supported by the National Institutes of Health (grant P01CA163233), the California Department of Public Health and the Centers for Disease Control and Prevention. Kurian has received research funding from Invitae, Myriad Genetics, Ambry Genetics, GenDx and Genomic Health. Stanford's departments of Medicine and of Health Research and Policy also supported the work. The Stanford University School of Medicine consistently ranks among the nation's top medical schools, integrating research, medical education, patient care and community service. For more news about the school, please visit http://med. . The medical school is part of Stanford Medicine, which includes Stanford Health Care and Stanford Children's Health. For information about all three, please visit http://med. .


News Article | March 29, 2016
Site: www.fastcompany.com

The cost of genetic testing has plummeted, but it's still out of reach for thousands of patients. But today, a San Francisco-based biotech company, Invitae, is expanding its suite of tests for neurological disorders, rare diseases, and pediatric conditions at a price point that is designed to be affordable to most people. Invitae already offers panels, or groups of tests, for a variety of genetic disorders in cardiology, neurology, and pediatrics. It also offers genetic tests to assess a patient's risk for hereditary cancers such as breast, colon, and pancreatic cancer. In the past few years, it increased its analysis from 200 genes in production to 1,000, meaning it is able to glean a vast amount of genetic content. What stands out is the company's pediatric screening, which is designed to complement routine newborn screenings. Today, millions of babies in the U.S. are tested for genetic, endocrine, and metabolic disorders. But about one in every six infants gets a false positive result, according to Invitae's chief medical officer Robert Nussbaum, who is a practicing medical geneticist at UC San Francisco. Invitae's pediatric tests examine whether the results are true positives, and, if so, hone in on the best course of treatment. "This development is pointing to the day when we can very quickly test newborns for any genetic condition that might put them at risk early in life," says Nussbaum. Invitae, a five-year-old company that went public in 2015, is one of a growing number of companies that is taking advantage of the plummeting cost of whole genome sequencing. In 2011, the late Apple CEO Steve Jobs spent $100,000 to find out the genetic roots of the cancer that later killed him. Now, an equivalent test would be available for about $5,000. But Invitae's competitive edge, according to its CEO Randy Scott, is that it's "aggregating a large number of genetic tests into a single platform." Today, a lab tests patients gene by gene. That gets expensive when the patient has a multi-genetic disease, or a set of symptoms that are caused by a variety of genetic conditions. "Historically just a single gene test is in the $1,000 range," says Scott. "We look at up to one thousand genes, which gives us improved economics. We hope to one day become the Amazon of medical genetics," he explains. The highest-price for a genetic test offered by Invitae is $1,500 for out-of-network providers. Most in-network tests are available at $950, with a discount offered to patients who don't have insurance. Patients are required to have a prescription from a doctor, which in many cases is a medical geneticist rather than a pediatrician or primary care doctor. (As we recently reported, many doctors are not educated about the still-nascent field of genetics.) The company is currently losing money on each of the tests it offers. But by the end of 2016, Scott expects that the company will start making money. "Genetics is a volume-dependent business," he says. "We hope to flip to being profitable."


News Article | December 7, 2016
Site: www.businesswire.com

SAN FRANCISCO--(BUSINESS WIRE)--Invitae Corporation (NYSE:NVTA), a genetic information company, today announced the expansion of its Breast Cancer STAT Panel with the addition of two important breast cancer predisposition genes – ATM and CHEK2 – and a faster turnaround time (TAT) with results available in as few as five days at no additional cost. The announcement was made at the San Antonio Breast Cancer Symposium (SABCS). “Recent research underscores the clinical utility of ATM and CHEK2 in making treatment decisions, and many of our provider clients have requested these genes be included,” said Robert Nussbaum, MD, chief medical officer of Invitae. “The addition of these genes to Invitae’s Breast Cancer STAT Panel provides clinicians with more comprehensive information without sacrificing time for results, ultimately supporting better patient care for patients and clinicians who need answers to help guide surgical decisions.” Invitae’s Breast Cancer STAT Panel includes seven well-established genes associated with a significantly increased risk of developing breast cancer: BRCA1, BRCA2, CDH1, PALB2, PTEN, STK11, and TP53. Invitae now offers the opportunity to add either or both ATM and CHEK2 based on research showing that each has important implications for understanding risk and guiding treatment decisions. The presence of a variant in any one of these nine genes, or a combination of them, may influence the patient and clinician choice between mastectomy and lumpectomy, whether to perform prophylactic salpingo-oophorectomy, and may inform choice of chemotherapy, including PARP inhibitors. Results for the expanded Breast Cancer STAT Panel are available in as few as five calendar days (average turnaround is seven). In order to provide clinicians with flexibility, Invitae will also provide testing for BRCA1 and BRCA2 only if desired with the same STAT turnaround time. Invitae also offers the ability to re-requisition additional cancer genes within 90 days at no additional charge. "When I ask most of my newly diagnosed breast cancer patients when they want surgery, their most frequent response is 'yesterday,'" said Barry Rosen, MD, breast cancer surgeon at Advocate Health in Barrington, Illinois. “Prior to Invitae's STAT testing, my patients were faced with the difficult choice to wait as long as a month for the testing to return before proceeding with surgery, or, more commonly, making a decision based on chance rather than science. Having a one week turnaround has dramatically improved my ability to care for my patients." Invitae’s Breast Cancer STAT Panel has the same high quality as Invitae’s current validated, hereditary cancer tests. Data published in the Journal of Molecular Diagnostics demonstrated the analytical accuracy (100%) and clinical concordance (99.8% compared to results from Myriad Genetics) of Invitae’s methods in a study of more than 1,000 patients in collaboration with Massachusetts General Hospital and the Stanford University School of Medicine. In addition, data showing the clinical utility of the Invitae hereditary breast and ovarian cancer (HBOC) panel test was published in a companion manuscript in JAMA Oncology. The additional genes are available at no additional charge and testing is available for both blood and saliva samples. The company recently announced agreements with the top five largest insurers in the United States, providing greater access for patients than ever before. Invitae’s transparent and affordable patient-pay option of $475 will continue to be available. As a matter of policy, Invitae does not hold samples or findings reports while managing insurance claims. “It is now so easy to just schedule my patients’ surgeries only one to two weeks into the future knowing full well that the Invitae STAT test will have returned results before the procedure to confirm which is the best surgical option,” said Paul Baron, MD, FACS, Breast and Melanoma Specialists of Charleston. “It has totally changed how I manage newly diagnosed patients.” Clinicians are able to access Invitae’s Clinical Consult Service through the entire testing process to select the right test, clarify results, and review individual patient cases at no additional charge. Invitae also makes telephone genetic counseling services available to patients before and after testing by clinician request. Invitae Corporation's (NYSE:NVTA) mission is to bring comprehensive genetic information into mainstream medical practice to improve the quality of healthcare for billions of people. Invitae’s goal is to aggregate most of the world’s genetic tests into a single service with higher quality, faster turnaround time, and lower price than many single-gene and panel tests today. The company currently provides a diagnostic service comprising hundreds of genes for a variety of genetic disorders associated with oncology, cardiology, neurology, pediatrics, and other rare disease areas. For more information, visit our website at invitae.com. This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995, including statements relating to Invitae’s STAT panel influencing surgical decisions and treatment options and supporting better patient care. Forward-looking statements are subject to risks and uncertainties that could cause actual results to differ materially, and reported results should not be considered as an indication of future performance. These risks and uncertainties include, but are not limited to: risks associated with the company’s ability to use rapidly changing genetic data to interpret test results accurately, consistently, and quickly; the company’s history of losses; the company’s need to scale its infrastructure in advance of demand for its tests and to increase demand for its tests; the company’s ability to develop and commercialize new tests and expand into new markets; the risk that the company may not obtain or maintain sufficient levels of reimbursement for its tests; laws and regulations applicable to the company’s business, including state licensing requirements and potential regulation by the Food and Drug Administration; and the other risks set forth in the company’s filings with the Securities and Exchange Commission, including the risks set forth in the company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2016. These forward-looking statements speak only as of the date hereof, and Invitae Corporation disclaims any obligation to update these forward-looking statements. NOTE: Invitae and the Invitae logo are trademarks of Invitae Corporation. All other trademarks and service marks are the property of their respective owners.


News Article | April 20, 2016
Site: www.fastcompany.com

Leslie Parks* was 34 and ready to start a family, but struggled for a year and a half to conceive. Before embarking on fertility treatments, her doctor required that she and her husband get screened to determine their carrier status for various genetic diseases. He recommended a Silicon Valley-based startup called Counsyl and assured her that the test would be fully covered by her insurance. Weeks later, Parks received a bill for more than $1,494 after her insurer deemed the test "experimental." Parks was shocked. As she later learned, that is the rate that Counsyl charges insurance companies; by contrast, their fee for uninsured patients is $349. Under Counsyl's guidance, Parks entered into a lengthy appeals process with her insurance company, writing letters and making phone calls for months. She asked Counsyl representatives if she could pay the uninsured patient rate of $349, but they declined and insisted she press ahead with the appeals process. More than six months later, her insurance company upheld their denial of the claim, and she was still faced with the $1,494 bill. She called Counsyl and asked again to pay the $349 uninsured patient fee instead. The representative finally agreed. In the meantime, Parks got pregnant. Two months into her pregnancy, her ob-gyn recommended that she have an advanced version of the routine prenatal testing. While Parks didn't have any high-risk factors, she would be 35 years old by the mid-point of her pregnancy, putting her in the "advanced maternal age" category. Her doctor said this would qualify her for a blood test at 11 weeks to determine whether her unborn child was at high risk of genetic conditions like Down Syndrome. Again, she was informed by her doctor that her insurance company would pick up the tab, or at the very most she'd have to pay a "couple hundred dollars" if the test was out of network. Yet a few weeks later, "basically the exact same thing happened again," she says. But this time, Parks received an $8,000 bill. The company, Natera, based in San Carlos, California, and founded in 2004, was a little more forthcoming when Parks called, distraught that she'd have to pay such a large sum. She says that Natera promised that they would handle the appeals process with her insurance company. If the claim was denied, however, they would send her another $8,000 bill but she could call and ask to pay the patient adjusted rate of $200. She asked if she would receive a bill for this adjusted amount. The representative said no, they wouldn't put that rate in writing. Parks says that the bills she received from both Counsyl and Natera made no indication that there was another tier of pricing, and it was only after calling and pressing for alternatives that the lower price was revealed. A Counsyl spokesperson says the company doesn't comment on individual patient cases, but that its goal is to offer transparency around billing. "Health care pricing is dynamic and complicated, but Counsyl is fully committed to providing patients with a clear and transparent assessment of screening costs," a statement reads. The company also pointed to its new billing section, which explains the process to patients. A Natera spokesperson says, "It is unfortunate that the patient . . . experienced shock at receiving such a big bill. However, in the health care industry, a company’s "list price" is typically substantially higher than the price ultimately paid by a patient. The final amount paid by a patient is dependent upon the price for the testing that was negotiated by the insurance company, the patient’s insurance plan’s coverage, and the plan’s associated copayment and deductible." Stories like Parks's are becoming increasingly common as hundreds of genetic tests flood the market. Forums for new and expecting parents, like Babycenter.com, are now filled with endless comment threads of patients fighting their insurance company after a claim is denied, or sharing feelings like being "misled" or "used" by the genetics companies, their doctors, their insurance—or a combination of the three. The crux of the problem is that genetic testing has exploded, but regulation has been slow to catch up. The U.S. Food and Drug Administration is still finalizing its guidance for how it will oversee the category of lab-developed tests, which includes some 60,000 genetic testing products already on the market. Furthermore, insurance companies are in the midst of determining whether to reimburse for all or part of the cost of genetic tests that do not offer clear diagnoses, but instead dabble in probabilities. Some insurers have opted to cover genetic tests in cases where the patient is deemed high risk (a common case is the breast cancer risk test, which insurers tend to pay for only when the patient has a family history of cancer). Other insurance companies will only reimburse for tests that it determines are "medically necessary." "Insurance coverage of genetic testing is an underappreciated, but huge and important question," says Patti Zettler, an associate professor at Georgia State University College of Law, who specializes in health policy. According to Zettler, coverage will vary depending on the person's medical history, their employer, and the state that they live in. The final bill is also dependent on the patient's deductible, whether they meet certain medical criteria, and whether the testing company is in-network or out-of-network. "Private insurance companies can essentially make their own decisions about what are medically necessary services and what are not," Zettler explains. And these decisions aren't particularly clear cut to anyone, let alone patients. "You've put your finger on why we got out of the reimbursement business," says Troy Moore, chief strategy officer for Kailos Genetics, in response to hearing Parks's story. "It was simply too frustrating for everyone involved." For two years, Kailos offered a reimbursement model. The company pulled in higher revenues overall by filing claims to insurers, but it also meant dealing with calls from confused and angry customers. According to Moore, many would demand the lesser, out-of-pocket rate after their insurance company rejected their claim, but it wasn't always that simple. Moore says many insurers don't have a problem with a genetics company offering a lower cash rate to patients who don't use insurance. The assumption is that it is cheaper to avoid insurance, as there's no administrative burden in filing and dealing with claims. But that doesn't apply to cases in which the claim has already been filed and rejected by the insurance company; in that case, it's harder to justify a vastly different cost for the patient. Moore says it might be considered fraudulent to overbill the government in cases where the patient is using Medicare or Tricare. For these reasons, his team recently made the decision to offer all their tests for a flat rate of a few hundred dollars. No insurance. No angry phone calls. No tedious billing process, which might involve faxing forms to insurers that are filled out with the requisite blue ink. But that also meant taking a good portion of the company's revenues off the table, which had to somehow be replaced. "Now, to make the same amount of money, we have to reach a lot of people and keep them happy," says Moore. "If they order once, we hope that they'll order again." Other genetic-testing companies remain divided on the question of whether to accept insurance and the hassle that comes with it. Most have settled on a mix of insurance (with different rates for in-network and out-of-network), flat cash rates, and financial assistance for those who need it. In that category: Counsyl, Natera, Myriad Genetics, and Invitae. Others, like Color Genomics, are taking a similar approach to Kailos by refusing to take insurance altogether. For her part, Parks just wishes the process was more clear. During one of her countless phone calls she expressed her frustration, saying, "Can you imagine how upsetting it is to be surprised with an $8,000 bill?" The representative replied, "Yes, I imagine so." *Parks requested to use a pseudonym, as she is still in the negotiations process.


News Article | November 17, 2016
Site: www.businesswire.com

SAN FRANCISCO--(BUSINESS WIRE)--Invitae Corporation (NYSE: NVTA), a genetic information company, today announced that members of the company’s management team will present at the Canaccord Genuity Medical Technology & Diagnostics Forum on Thursday, November 17, 2016 at approximately 3:00 p.m. Eastern at the Westin Grand Central in New York City. The live, listen-only webcast of the presentation may be accessed by visiting the investors section of the company’s website at ir.invitae.com. A r


News Article | February 21, 2017
Site: www.prnewswire.com

SAN FRANCISCO, Feb. 21, 2017 /PRNewswire/ -- Invitae Corporation (NYSE: NVTA), one of the fastest growing genetic information companies, today announced that members of the company's management team will present at the Cowen and Company 37th Annual Health Care Conference on Monday, March...


Systems and methods for biological sample processing are described. A production line extracts genomic DNA from a biological sample, amplifies target components of the sample and produces sequence data for markers from the amplified components. The markers are associated with tests identified in a requisition received with the sample and some markers may be associated with unrequisitioned tests. A sample information management system (SIMS) controls and monitors the production line and subsequent analysis of the results using information in a quality control (QC) database to validate the results. A repository comprising the QC database and a research database receives and aggregates the results without identifying the source of the sample. A portal may be provided to provide access to the research database to a plurality of external contributors. Contributors can selectively provide additional research data and data can be processed using data mining and curation tools.


Provided herein are novel methods, systems and processes for mapping sequence reads to a modified reference genome and determining the presence or absence of a genetic variation, or the likelihood thereof, in a gene of interest in a subject.


Patent
Invitae | Date: 2013-12-06

Methods for multiplex ligation-dependent probe amplification include (a) providing a sample tissue to query different target nucleic acids, (b) providing different probe sets for each of the target nucleic acids, each probe set including a first locus specific probe having a first adapter sequence and a first target specific portion and a second locus specific probe having a second adapter sequence, and a second target specific portion adjacent to the first target specific portion, (c) hybridizing the probe sets to the target sequences to form hybridization complexes, (d) ligating the hybridization complexes to form ligated probes, (e) amplifying the ligated probes to form amplicons, the amplifying step being carried out with a first universal primer including a region complementary to the first adapter sequence and a second universal primer including a region complementary to the second adapter sequence, and (f) detecting the amplicons in a detection system by sequencing each of the amplicons.


SAN FRANCISCO, Dec. 21, 2016 /PRNewswire/ -- Invitae Corporation (NYSE: NVTA), a genetic information company, today announced the availability of 24 new and 19 expanded genetic test panels, allowing clinicians to gain information on 183 new genes with clinical and diagnostic significance....

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