Jan Marshall Friedman
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* Improving the sensitivity of whole genome sequencing as a clinical test for genetic causes of intellectual disability
* Development and evaluation of genetic e-counselling for clinical whole genome sequencing
* Which maternal medications can harm the developing human embryo?
* Improving the clinical care of patients with neurofibromatosis 1, an autosomal dominant multisystem disease
Graduate Student Supervision
Doctoral Student Supervision (Jan 2008 - May 2019)
Neurofibromatosis 1 (NF1) is an autosomal dominant disorder with an estimated prevalence of 1/3000. NF1 is characterized by multiple café-au-lait spots, iris hamartomas, and multiple nerve sheath tumors. Patients may also present with heart disease, cerebrovascular disease, ischemia, or aneurysm. Though well documented, vascular disease in NF1 patients remains poorly understood. Previous in vitro studies suggest that endothelial and vascular smooth muscle function is altered in Nf1+/- mice; however, it is unknown how these alterations affect vascular function in vivo. Haploinsufficiency for neurofibromin, the protein affected in patients with NF1, results in prolonged Ras hyperactivation. We hypothesized that this may result in vascular endothelial dysfunction and impaired cardiac function. To study this hypothesis we examined vascular function in Nf1+/- and control mice using wire myography. Isometric force measurements in thoracic and abdominal aorta at 6-months of age were similar, with Nf1+/- mice demonstrating altered smooth muscle function, enhanced relaxation, and upregulation of the PI3K/Akt/eNOS pathway. To determine if the alterations observed at 6 months of age remain stable or progress to a more dysfunctional state, we examined the abdominal aorta in older mice. Interestingly, we observed increased contraction and reduced relaxation in 9-to-12 month old Nf1+/-mice compared to control littermates, indicative of endothelial dysfunction and progression to a more dysfunctional state. Vascular dysfunction is likely to impact cardiac performance, and Ras hyperactivation has also been linked to cardiac dysfunction. We, therefore, used 2-dimensional echocardiography with color Doppler to measure cardiac function in Nf1+/- and control littermates. We found that Nf1+/- mice have increased left ventricular wall thickness and reduced cardiac contractility. We also observed alterations in cardiomyocyte organization in Nf1+/- animals. The results presented in this thesis support the hypothesis that neurofibromin haploinsufficiency in Nf1+/- mice results in vascular endothelial and cardiac dysfunction. Whether these findings extend to humans with NF1, who have the same genetic defect, is unknown, but if so, our observations may have important clinical implications. The role of neurofibromin in other kinds of vascular disease needs to be studied, and the possibility that neurofibromin may provide a novel therapeutic target should be explored.
Intellectual disability affects 1-3% of individuals globally, and, for half the cases, the cause is unknown. Recent studies using whole genome microarray genomic hybridization have shown that submicroscopic genomic imbalance causes intellectual disability in at least 10% of idiopathic cases with normal conventional cytogenetic analysis. I established genotype-phenotype correlations for de novo copy number variants detected by previous whole genome array genome hybridization studies performed by our group in children with intellectual disability. These genotype-phenotype correlations show that genomic imbalance of genes belonging to the epigenetic regulatory category, among others, are causative of intellectual disability. I hypothesized that dosage changes in the broad functional category of genes encoding epigenetic regulatory proteins are more likely to be pathogenic for intellectual disability than dosage changes in other kinds of genes. Epigenetic regulatory proteins include those with DNA methylation, histone modification or chromatin remodeling activity. I have selected all known genes encoding epigenetic regulatory proteins and defined probes to interrogate these candidate genes for copy number alteration as part of a custom targeted microarray design that selectively investigates all candidate genes associated with intellectual disability. We have conducted comparative genome hybridization on 177 patients with idiopathic intellectual disability using this array and on both normal parents of each affected child. We identified and independently validated 16 cases with de novo CNVs involving the epigenetic regulatory candidates. 7 of the 16 CNVs involve the same exon of the JARID2 gene, while the other 9 CNVs affect different genes. I discuss genotype-phenotype correlations for these cases and show that epigenetic perturbation by way of disruption of genes that encode epigenetic regulators is an important cause for intellectual disability.
Major birth defects occur in 2% to 3% of liveborn infants and are the leading cause of infant mortality. The cause of most birth defects is unknown. The objectives of this thesis are to (1) assess the risk of having a birth defect in human pregnancy following maternal use of common antidepressant medications and to (2) evaluate the risk of a birth defect or subsequent adverse outcome in relation to restricted fetal growth in early pregnancy. I used data from the National Birth Defects Prevention study, a population-based case-control study of birth defects risk factors in the US to study the rates and patterns of antidepressant medication use around pregnancy and compare the prevalence of common antidepressant medication use among mothers of cases and mothers of controls. I found that selective serotonin reuptake inhibitors (SSRIs) were the most commonly used antidepressants among pregnant women, followed by bupropion, and that the rate of maternal antidepressant use significantly increased over the period between 1998 to 2005. I found that maternal use of SSRIs in early pregnancy was associated with the occurrence of anencephaly, craniosynostosis and omphalocele in the infant, whereas early pregnancy exposure to bupropion was associated with an increased risk for left outflow tract heart defects. I also conducted a retrospective cohort study using ultrasound examination data on singleton pregnancies in women with regular menstrual cycles who had crown-rump length (CRL) measurements at the Ultrasound Unit of British Columbia Women’s Hospital. I found that a first trimester CRL in the 10th centile or less was strongly associated with subsequent spontaneous abortion, delivering through a cesarean section or having an infant with low birth weight or length. The results presented in this thesis indicate that maternal treatment with common antidepressant medications may increase the risk for certain birth defects and that restricted growth of the embryo may adversely affect subsequent pregnancy outcomes.
Master's Student Supervision (2010 - 2018)
The vast majority of the human genome (~98%) is non-coding. A symphonyof non-coding sequences resides in the genome, interacting with genes andthe environment to tune gene expression. Functional non-coding sequencesinclude enhancers, silencers, promoters, non-coding RNA and insulators.Variation in these non-coding sequences can cause disease, yet clinical sequencing in patients with rare Mendelian disease currently focuses mostly on variants in the ~2% of the genome that codes for protein. Indeed,variants in protein-coding genes that can explain a phenotype are identified in less than half of patients with suspected genetic disease by wholeexome sequencing (WES). With the dramatic reduction in the cost of wholegenome sequencing (WGS), development of algorithms to detect variantslonger than 50 bp (structural variants, SVs), and improved annotation ofthe non-coding genome, it is now possible to interrogate the entire spectrumof genetic variation to identify a pathogenic mutation. A comprehensive pipeline is needed to analyze non-coding variation andstructural variation from WGS. In this thesis, I developed and benchmarkeda bioinformatics workflow to detect pathogenic non-coding SNVs/indels andpathogenic SVs, and applied this workflow to unsolved patients with rareMendelian disorders. The pipeline detected ~80-90% of deletions, ~90% ofduplications, ~65% inversions, and ~50% of insertions in a simulated genomeand the NA12878 genome. The pipeline captured the majority of knownpathogenic non-coding single nucleotide variant (SNVs) and insertion deletions(indels), and selectively prioritized a spiked-in known pathogenic non-codingSNV. Several interesting candidate variants were detected in patients,but none could be convincingly implicated as pathogenic.The bioinformatic workflow described in this thesis is complementary tosequencing pipelines that analyze only protein-coding variants from wholegenomes. Application of this workflow to larger cohorts of patients with rareMendelian diseases should identify pathogenic non-coding variants and SVsto increase diagnostic yield of clinical sequencing studies, assist managementof genetic diseases, and contribute knowledge of novel pathogenic variants to the scientific community.
Introduction: Gliomas in the brain and the optic pathway affect up to 20% of all children with neurofibromatosis 1 (NF1); however, their frequency and natural history in adults is poorly described. Our objectives were to characterize the frequency and natural history of gliomas seen in NF1 patients by serial head magnetic resonance imaging (MRI) and to investigate associations between combined annotation-dependent depletion (CADD) scores and the presence of MRI features of NF1.Methods: 1775 head and whole-body MRI scans of 562 unselected NF1 patients were collected at the University Hospital Hamburg-Eppendorf in Hamburg, Germany. All scans were analyzed, and the frequency and natural history of gliomas was determined. In addition, the constitutional disease-causing variants of the NF1 gene in 283 patients were annotated with CADD scores, and genotype-phenotype correlations were performed.Results: Between 1 and 12 MRI scans were collected for each patient; the median length of follow-up was 3.7 years. We found the prevalence of non-optic gliomas to be 4.3%, with a median age at glioma diagnosis at 21.2 years. The prevalence of optic pathway gliomas (OPGs) was 9.3%, with a median age at diagnosis at 12.1 years. We determined the rates of appearance, progression and regression of both of these tumour types. We found that individual CADD scores were associated with the presence of plexiform neurofibromas (but not with the presence of UBOs or optic gliomas) in NF1 patients in whom the pathogenic mutation had been identified. Conclusion: The frequencies of gliomas in the brain and optic pathway is higher in adults with NF1 than previously reported. NF1 patients with constitutional mutations associated with high CADD scores appear to be at higher risk to develop plexiform neurofibromas than other NF1 patients.