Michael M. Segal, M.D. Ph.D. - US grants

DESCRIPTION (provided by applicant): Automated genome-phenome analysis The declining cost of whole exome sequencing (WES) is nearing the point at which the spread of WES into clinical practice will be limited largely by the cost of interpreting the results and comparing the to the patient's clinical findings. This project tests the feasibility of reducing this interpretaton cost by pairing automated genome sequencing with an automated comparison of the patient's findings to the phenotype of findings of known diseases. This uses the SimulConsult diagnostic tool to provide phenome analysis, and then integrate with genome analysis results to provide an automated genome-phenome analysis. Aim 1 is to compute unified severity scores for genome-phenome analysis so as to replace the current methods, which use iterative manual modifications of Boolean filtering of variants. The new approach is a one- pass method based on quantitative severity scores that are then processed by comparison to the phenome. This approach combines many assessments of gene variants provided by SeattleSeq, including conservation scores, read quality scores and variant frequency in the population, to automatically construct quantitative severity scores. To refine the quantitative severity score input weightings, 10 patients will be analyzed for whom SimulConsult has already been used to assist in diagnosis. This builds upon the ability added in 2012 to SimulConsult to import and process the variant table of WES results that includes the HGNC gene name, severity score, and zygosity. Also, the ability will be added to import more than one variant table and compute with the intersection (i.e., variants present in both) so familial genetic information can be incorporated. Aim 2 is to assess the effectiveness of automated genome-phenome analysis to identify known disease- causing genes in patients by retrospectively analyzing 20 patient cases in which WES was already performed on a family with two or more affected members and a known disease-causing mutation was found. The diagnostic accuracy will be assessed by (1) the rank of the correct diagnosis and (2) the probability assigned by the software. This will compare the genome alone, phenome alone, and genome + phenome approaches, as well as other situations involving incidence and onset ages. Aim 3 is to determine the need for having genomes from others in the family, by assessing differences between examining only the proband versus utilizing information on a second affected family member. The overall goal is to create and test the capability for making WES more practical to analyze and more accurate by integrating phenome information with the genome information, combining two independent assessments of the diagnosis. Today, interpretation costs exceed reimbursement rates, and interviews with relevant labs suggest need for lower costs. As the phenotype becomes known for a greater fraction of genetic abnormalities, the applicability of the automated genome-phenome analysis and the market for it will grow.

DESCRIPTION (provided by applicant): The declining cost of whole exome sequencing (WES) is nearing the point at which the spread of WES into clinical practice will be limited largely by the cost of interpreting the results and comparing them to the patient's clinical findings. This project builds on our demonstrated capability to reduce this interpretation cost by pairing our diagnostic software, in wide use for clinical diagnosis, with automated genomic sequencing. The clinical diagnostic software compares patients to phenotypes of findings in known diseases, so the combination with genome analysis, developed under an SBIR Phase 1 grant, is referred to as automated genome-phenome analysis. This award-winning capability is valued because of its ability to analyze genomes in seconds, and its hypothesis-independent nature. Here we propose to advance the genome-phenome analysis as follows: Aim 1 is to generalize the analysis beyond the trio (affected individual plus parents) in order to support a wider variety of family structures. These include nuclear families with more than one sibling, families that extend beyond the nuclear family and unrelated affected individuals. These capabilities will be useful in both clinical diagnosis and discovery of new connections between genes and diseases. These capabilities will be added in a way that preserves the speed and hypothesis-independent nature of the analysis. Aim 2 is to detect copy number variation (CNV) using exomes and analyze that genomic data in the clinical context. Using WES for CNV analysis will lower the cost of diagnosis by reducing the need to order a microarray before exome analysis, and will facilitate the automated analysis of DNA deletions and duplications in clinical care. Aim 3 is to improve the core analysis by taking into account which genes were well-read but normal, information that is important in excluding other diagnoses. The analysis will also deal with situations of ambiguity over whether an affected individual is homozygous or heterozygous, and do so in a way that only adds possibilities for diagnosis but doesn't reduce possibilities considered by the original analysis. Aim 4 is to improve output by reporting on incidental findings and exporting information in ways that facilitate interactions with referring physicians and reporting of genome variants to public databases. The overall goal is to improve accuracy and reduce the time and cost of analysis, making WES more robust as a clinical tool, as well as a tool for gene discovery. Today, interpretation costs exceed reimbursement rates, and interviews with labs suggest that the major reason for high costs is the manual nature of the clinical correlation, which we automate. As the phenotype becomes known for a greater fraction of genetic abnormalities, the applicability of our automated genome-phenome analysis and the market for it will grow.

We have described an autosomal dominant syndrome that we call ?Sensory Overstimulation Syndrome? (SOS). The most distinctive feature is the relative ineffectiveness of the local anesthetic lidocaine, a drug that blocks sodium channels. The 3 other key findings, based on characterization of 180 patients, are inattention, painful muscle cramps, and in females, severe Premenstrual Syndrome (PMS). We estimate that SOS affects 3% of the entire population, or ~9 million people in the USA, which would make this syndrome among the most frequent causes of each of these diverse findings, providing a genetic diagnosis for many who had previously been given non-syndromic diagnoses such as ADHD or PMS. We have developed a biological test kit for the lidocaine ineffectiveness that is simple, non-invasive, not painful, and non- gameable by people who are normal but trying to obtain drugs of abuse. The diagnostic test kit prototype has been tested in a small study (n=19). It has been protected with a patent filing and the FDA has asked us to validate the test kit in controlled trials before filing for marketing approval. The importance of this test goes beyond a reaching a correct diagnosis and selecting alternate local anesthetics. SOS patients with inattention respond well to potassium treatments, reducing the need for stimulants. We expect impact on drug abuse, premenstrual syndrome, and severe pain due to dental treatment in people with lidocaine ineffectiveness, often dismissed as if it were due to ?dental anxiety?. We propose the following: Aim 1: Assess reliability of taste-based lidocaine test kit in a controlled trial and compare to lidocaine injection. The ability of lidocaine oral gel to block taste (salt and sucrose solutions) will be assessed in 10 adults and then 10 teenagers, half each with history of lidocaine ineffectiveness. The painless taste-based lidocaine test will be evaluated in a randomized controlled trial, tested 4 times on different days for each subject to determine the reproducibility. At the FDA's request, each subject will also have the ?gold standard? of injection of lidocaine, assessed using pain, for comparison. Aim 2: Use the test kit to determine the prevalence of lidocaine ineffectiveness in the general population. We will use the test kit to determine the prevalence of lidocaine ineffectiveness by studying 100 individuals ages 13-49 with no diagnosis of inattention to characterize the prevalence in the general population (expect ineffective in ~2%). Aim 3: Use the test kit to determine the prevalence of lidocaine ineffectiveness in patients with ADHD. Using the test kit, we will test the association between lidocaine ineffectiveness and inattention by studying 80 individuals ages 13- 49 with inattention, chosen from those who had been diagnosed with ADHD (expect ineffective in ~30%). We expect that this lidocaine test will provide a mechanistic biomarker for identification of the SOS syndrome in significant fractions of people currently diagnosed as having ADHD or PMS. Given the apparent high prevalence of SOS, the potential of the lidocaine taste test kit for commercialization is high, as is the impact on public health.