A Quarterly Newsletter from GeneInsightIssue 3: July 2014
We are pleased to share the Summer 2014 edition of our newsletter, GeneInsights. In this edition, we feature a Q&A session with Lisa Edelmann, Ph.D., from Mt. Sinai Genetic Testing Laboratory and we highlight the c.-3133G>T variant in the MUC5B gene as part of our ongoing Featured Assessment series.
We hope you enjoy the latest issue of GeneInsights. Happy Summer!
Q and A Session with Lisa Edelmann, Ph.D., Director of the Mount Sinai Genetic Testing Laboratory, Associate Professor, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai
Dr. Edelmann received her B.S. in Biochemistry from the State University of New York at Stony Brook and her Ph.D. in Molecular Genetics from The Albert Einstein College of Medicine. Dr. Edelmann is certified in Clinical Molecular Genetics and Clinical Cytogenetics by the American Board of Medical Genetics and Genomics (ABMG).
What do you think are the major challenges for genetic and genomic testing laboratories as the field scales to higher complexity and higher volume tests?
Everyone is thinking about this right now because tests are becoming more and more complex. I think informatics infrastructure is critically important. Since most of the higher-complexity tests are next generation sequencing (NGS) based and usually generate large amounts of sequence data across many genes, it’s really important that the process be as automated as possible. From the data generation through the pipeline, even up to the point where you’ve identified a variant and are confirming the findings - a good informatics infrastructure can streamline the process so that you don’t need to sift unnecessarily through large amounts of data which can be very time consuming.
Part of having robust informatics is building out your bioinformatics. There are some interesting tools available that aggregate information from multiple databases and provide you a score for the likelihood a variant causes disease. People are also starting to think about effectively combining those sources into one tool so you don’t have to look at 5 or 6 different databases. Having easy and centralized access to all of the relevant analysis tools, variant databases, population sequencing data and internal databases is essential; otherwise the workflow becomes very cumbersome.
Another challenge is content expertise. Generally, when you’re reporting on the same disease set all the time, especially from a Clinical Laboratory Geneticist’s point of view, you become an expert on the disorders you’re covering. As testing becomes more complex and involves many more genes, particularly with exome or genome tests, the model changes and you need broad expertise across multiple distinct disease disciplines.
Lastly, I would raise reimbursement as a key challenge. Since I’m a Laboratory Director, I think about the financial aspects of the lab quite a bit - I have a large staff and I need to think about salaries and the overall budget. With genomic testing, the more genes you add to a panel doesn’t necessarily translate to greater reimbursement. Larger more complex panels may not get reimbursed more than smaller panels given the existing caps on reimbursement even though these tests may require more labor and effort. When you get to whole exome or whole genome tests, the reimbursement gets even more complex and unclear.
Can you tell me about some of the testing menu changes going on in your laboratory and what was the impetus for this change?
Our laboratory covers all three genetic disciplines: biochemical genetics, cytogenetics/cytogenomics and molecular genetics. The biggest changes are going on in the molecular lab. All of our tests are moving toward NGS. We have at least 20 NGS panels in production right now and 5 that are currently being used. Even our carrier screening panel, which traditionally has been performed on a genotyping platform, is being transferred to an NGS platform. The benefit of this shift is that you are no longer just looking at your targeted founder mutations or most common set of mutations; you’re able to scan the whole gene and discover mutations you wouldn’t otherwise find allowing for more comprehensive screening.
Since its inception, our molecular laboratory has been involved in carrier screening, and our main products are the carrier screening panels. Shifting to NGS for them is challenging because carrier screening needs to be completed in 7-10 days, while most NGS tests turnaround in 4-6 weeks. The turnaround times for carrier screening need to be much faster than typical NGS tests, but we really need to move toward NGS and away from genotyping tests in order to offer patients, more complete information.
We also added whole exome sequencing in the past year, which was a major undertaking for the lab. Setting up whole exome sequencing involved collaboration across our Clinical Department, Genomics Institute, and Core Lab, which is very different than how it’s normally done. The Physicians and Genetic Counselors in the Clinical Genetics Division were instrumental in formulating the consent process, the Clinical Genomics Core performed the sequencing, while the Institute for Genomics and Multiscale Biology devised the pipeline and helped to build the infrastructure for data analysis. This is a departure from the normal process which usually involves a much smaller number of individuals all of which have a primary affiliation with the Genetic Testing Laboratory.
Can you share more about your Ashkenazi carrier test?
We just launched a brand new expansion of our Ashkenazi Jewish panel, which is one of the things that the lab has pioneered. We have been offering expanded carrier screening with Counsyl for 100 disorders, but the panel isn’t really focused on the Ashkenazi Jewish population, so we took it upon ourselves to comb the literature to find additional disorders that were clearly associated with the Ashkenazi Jewish population or common mutations that seemed to be pan-ethnic. In addition, in collaboration with Physicians in our Clinical Genetics Division, we identified mutations in Ashkenazi Jewish patients that were either novel or previously undescribed in this population. We then screened over 2,000 individuals to understand the population frequency and determine if we should include these disorders on our carrier screening panel. This process proved important as several disorders dropped off the list due to no or limited frequency in the population we screened. Another disorder dropped off because it was too common, and we determined that it was a polymorphism, not really a mutation.
In the end we were left with 18 additional disorders that had a frequency between 1 in 36 for Smith-Lemli-Opitz syndrome to 1 in 373 for Arthrogryposis, mental retardation and seizures. So we expanded the existing Ashkenazi Jewish panel to 38 disorders up from the original 20 disorders, which also included Fragile X and SMA. The panel was created the using Sequenom MassARRAY technology and launched back in November.
The uptake has been mostly positive and the disorders are either severely debilitating in childhood, or progressive. In some cases there’s treatment available and early detection can be very helpful to avoid metabolic decomposition, such as in the case of Galactosemia.
What are the key drivers or barriers to widespread WES/ WGS adoption into clinical practice?
The main group of physicians that order our WES tests are Geneticists. We’ve had requests from some other departments at Mount Sinai but for the moment, it seems that the requests are being driven by the Genetics Community. I think that education around when it’s appropriate to order an exome and what the test can and can’t do, would be useful for certain other medical disciplines. Other Physician groups could be ordering these tests, but one of the challenges is that the consent process is very involved. It’s not easy for a Physician, who isn’t a Geneticist or at least connected to Genetics, to actually explain the consent. It involves multiple family members consenting to different types of information, so that’s a bit of a challenge, and it definitely requires genetic counseling to be part of the process.
An understanding of insurance reimbursement is also very important because it’s not a test that you can just order and expect to be covered. There’s a lot of effort that goes into figuring out whether the patient’s insurance will reimburse or not, and often it requires a letter from a physician. I also think the insurance companies and providers really need to be better educated about genomic testing so that reimbursement will not be such an impediment.
As a founding member of VariantWire, a data sharing initiative that leverages the GeneInsight IT infrastructure, how critical do you think data sharing will be to furthering the field of clinical genomics?
Understanding the relevance of the variants that are identified by large scale sequencing is a real challenge. Data sharing is critical to patient care because no single laboratory is going to have all of the information, especially when we move to whole exome sequencing as first tier test. In the same respect, no individual laboratory is going to have the kind of test volume to have a large enough database to easily classify variants for every single gene. Right now, ClinVar is very helpful, we are using it all the time. It will only improve when as more information is added.
Data sharing among the VariantWire participants is going to be very helpful to the members of the network. For example, one laboratory may have a lot of data on a particular disease and group of genes and another laboratory has a different set, and together they have a great data set that’s more comprehensive. I definitely think that being part of VariantWire is beneficial to our lab.
Our Featured Assessment is intended to highlight the assessment of a specific gene or variant as part of an ongoing series included in the GeneInsights newsletter. This segment will review the process of assigning significance to a variant or gene in the clinical and/or research setting.
Variant: c.-3133G>T in the MUC5B gene
Pulmonary medicine has had minimal integration between clinical diagnosis and molecular genetics, with the majority of testing in this subspecialty currently limited to genotyping for cystic fibrosis (CF) and alpha-1 antitrypsin (A1AT) deficiency. However, there are many pulmonary diseases that would benefit from genetic testing. To promote the diagnosis and treatment of inherited pulmonary disorders the Partners HealthCare Laboratory for Molecular Medicine (LMM) has recently launched the PulmoGene Panel, which is offered as a comprehensive testing panel of 57 genes implicated in various pulmonary diseases and is also available in phenotype-driven subpanels.
Clinical interpretation of a genetic risk factor:
In several individuals with pulmonary fibrosis, a heterozygous variant was identified in the MUC5B gene (NM_002458.2:c.-3133G>T, rs35705950). The Mucin 5, subtype B gene (MUC5B) codes for mucins, which are macromolecules that are the major component of mucus secretions. The c.-3133G>T variant is a single-nucleotide polymorphism (SNP) located in the promoter of the MUC5B gene. The promoter region is located upstream from the start site of the gene and is responsible for initiating and regulating the transcription of the MUC5B gene. The c.-3133G>T variant is associated with elevated MUC5B transcript levels in the lungs of patients with idiopathic pulmonary fibrosis (IPF). Although this variant is common in the general population, the frequency of this variant is much higher in the IPF population. Due to this data, the MUC5B promoter variant is thought to be a risk allele which puts those who carry a copy of the variant at an increased risk for developing IPF compared to individuals who do not carry the MUC5B variant.
The c.-3133G>T variant in the promoter region of MUC5B is prevalent in many populations (reported frequencies ranging between 0.5 and 13%; 1000 Genomes Project - http://www.ncbi.nlm.nih.gov/projects/SNP; rs35705950). This variant is not expected to cause highly penetrant, Mendelian disease on its own. However, it was shown to increase the amount of MUC5B mRNA (Seibold 2013) and the T allele has been reported to have a frequency of 41.9% in the IPF population and 10.8% in the control population (P=2.9x10^-44; Borie 2013). Several studies have reported that one copy of the variant allele (T) increases the risk of developing idiopathic pulmonary fibrosis (IPF) up to 6 fold (Borie 2013; Hunninghake 2013; Peljto 2013; Seibold 2013; Stock 2013), and two copies of the variant T allele (homozygous) increases the risk up top 21 fold (Borie 2013). In summary, this variant is considered a risk factor for IPF.
After synthesizing the data, the c.-3133G>T variant in MUC5B was classified as a Risk Allele. While it is not expected to lead to IPF on its own, it is likely acting in conjunction with other genetic and/or environmental risk factors to cause disease.
Borie R, Crestani B, Dieude P, Nunes H, Allanore Y, Kannengiesser C, Airo P, Matucci-Cerinic M, Wallaert B, Israel-Biet D, Cadranel J, Cottin V, Gazal S, Peljto AL, Varga J, Schwartz DA, Valeyre D, Grandchamp B. 2013. The MUC5B Variant Is Associated with Idiopathic Pulmonary Fibrosis but Not with Systemic Sclerosis Interstitial Lung Disease in the European Caucasian Population. PLoS ONE. 8(8):e70621.
Hunninghake GM, Hatabu H, Okajima Y, Gao W, Dupuis J, Latourelle JC, Nishino M, Araki T, Zazueta OE, Kurugol S, Ross JC, San José Estépar R, Murphy E, Steele MP, Loyd JE, Schwarz MI, Fingerlin TE, Rosas IO, Washko GR, O’Connor GT, Schwartz DA. 2013. MUC5B promoter polymorphism and interstitial lung abnormalities. N. Engl. J. Med. 368(23):2192-200.
Peljto AL, Zhang Y, Fingerlin TE, Ma SF, Garcia JG, Richards TJ, Silveira LJ, Lindell KO, Steele MP, Loyd JE, Gibson KF, Seibold MA, Brown KK, Talbert JL, Markin C, Kossen K, Seiwert SD, Murphy E, Noth I, Schwarz MI, Kaminski N, Schwartz DA. 2013. Association between the MUC5B promoter polymorphism and survival in patients with idiopathic pulmonary fibrosis. JAMA. 309(21):2232-9.
Seibold MA, Wise AL, Speer MC, Steele MP, Brown KK, Loyd JE, Fingerlin TE, Zhang W, Gudmundsson G, Groshong SD, Evans CM, Garantziotis S, Adler KB, Dickey BF, du Bois RM, Yang IV, Herron A, Kervitsky D, Talbert JL, Markin C, Park J, Crews AL, Slifer SH, Auerbach S, Roy MG, Lin J, Hennessy CE, Schwarz MI, Schwartz DA. 2011. A common MUC5B promoter polymorphism and pulmonary fibrosis. N. Engl. J. Med. 364(16):1503-12.
Stock CJ, Sato H, Fonseca C, Banya WA, Molyneaux PL, Adamali H, Russell AM, Denton CP, Abraham DJ, Hansell DM, Nicholson AG, Maher TM, Wells AU, Lindahl GE, Renzoni EA. 2013. Mucin 5B promoter polymorphism is associated with idiopathic pulmonary fibrosis but not with development of lung fibrosis in systemic sclerosis or sarcoidosis. Thorax. 68(5):436-41.
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