Massively parallel sequencing has rapidly revolutionized DNA and RNA research. Sample preparations are steadfastly advancing, sequencing costs have plummeted and throughput is ever growing. This progress has resulted in exponential growth in data generation with a corresponding demand for bioinformatic solutions. This thesis addresses methodological aspects of this sequencing revolution and applies it to selected biological topics. Papers I and II are technical in nature and concern sample preparation and data anal- ysis of RNA sequencing data. Paper I is focused on RNA degradation and paper II on generating strand specific RNA-seq libraries. Paper III and IV deal with current biological issues. In paper III, whole exomes of cancer patients undergoing chemotherapy are sequenced and their genetic variants associ- ated to their toxicity induced adverse drug reactions. In paper IV a comprehensive view of the gene expression of the endometrium is assessed from two time points of the menstrual cycle. Together these papers show relevant aspects of contemporary sequencing technologies and how it can be applied to diverse biological topics. / <p>QC 20160329</p>

During the last decade high throughput DNA sequencing of single cells has evolved from an idea to one of the most high profile fields of research. Much of this development has been possible due to the dramatic reduction in costs for massively parallel sequencing. The four papers included in this thesis describe or evaluate technological advancements for high throughput DNA sequencing of single cells and single molecules. As the sequencing technologies improve, more samples are analyzed in parallel. In paper 1, an automated procedure for preparation of samples prior to massively parallel sequencing is presented. The method has been applied to several projects and further development by others has enabled even higher sample throughputs. Amplification of single cell genomes is a prerequisite for sequence analysis. Paper 2 evaluates four commercially available kits for whole genome amplification of single cells. The results show that coverage of the genome differs significantly among the protocols and as expected this has impact on the downstream analysis. In Paper 3, single cell genotyping by exome sequencing is used to confirm the presence of fat cells derived from donated bone marrow within the recipients’ fat tissue. Close to hundred single cells were exome sequenced and a subset was validated by whole genome sequencing. In the last paper, a new method for phasing (i.e. determining the physical connection of variant alleles) is presented. The method barcodes amplicons from single molecules in emulsion droplets. The barcodes can then be used to determine which variants were present on the same original DNA molecule. The method is applied to two variable regions in the bacterial 16S gene in a metagenomic sample. Thus, two of the papers (1 and 4) present development of new methods for increasing the throughput and information content of data from massively parallel sequencing. Paper 2 evaluates and compares currently available methods and in paper 3, a biological question is answered using some of these tools. / <p>QC 20160127</p>

Next-Generation Sequencing has opened the doors to nearly limitless amounts of genomic data, but the clinical utility of this data is not yet clear. From examining at sequencing data of known familial cancer genes in hereditary cancer patients, the NCGENES study found a clear molecular diagnosis in about 5% of patients and an uncertain molecular result in about 15% of patients. The remaining 80% of hereditary cancer patients received a negative result for the screening of known cancer genes. These latter patients were followed up by whole exome sequencing analysis, and the data was used to perform a research sweep to potentially identify mutation(s) in gene(s) that have yet to be clearly associated with their phenotype. Hereditary breast cancer has a relatively well-established set of susceptibility genes, yet a large percentage of the molecular etiology is still unknown. There are many genes that are good candidates for breast cancer genes based on their protein's function, but they may not actually contribute to breast cancer susceptibility. The ClinGen consortium is aiming to establish the clinical validity of gene-disease associations so that clinicians and patients can better interpret and utilize sequencing results. Six breast cancer susceptibility genes were evaluated using the ClinGen clinical validity framework with the goal of both evaluating the genes already on hereditary breast cancer panels and evaluating genes not yet widely tested to determine if there is enough evidence to support their role in disease to warrant widespread testing. These genes have varying levels of evidence supporting their role in breast cancer susceptibility. The variants in each of the six genes were compared between a cancer patient cohort and a non-cancer patient cohort enrolled in the NCGENES whole exome sequencing study. One likely pathogenic variant and several variants of unknown significance were identified in various genes, and the burden of variants in cancer cases versus controls was evaluated, although the controls were not matched to the cancer cohort in any way. Research sweeps were performed for patients with VUSs to ensure that there were no other mutations in genes that would better fit the phenotype. This thesis presents a method for evaluating gene-disease associations and for utilizing whole exome sequencing data to pinpoint a molecular diagnosis in hereditary breast cancer patients. Overall, it was found that the ClinGen method of evaluating clinical validity of gene-disease associations could be helpful when determining if variants are pathogenic or benign. A new gene, RINT1, was found to have enough evidence to be moderately associated with hereditary breast cancer and it was subsequently added to the diagnostic list so that all cancer patients will now be screened for RINT1 variants. In addition, it was found that two of the genes currently on the diagnostic list, RAD51C and RAD51D, have "disputed" evidence with respect to breast cancer susceptibility. Interestingly, they have much more evidence for an association with ovarian cancer, so if variants are found in these genes, the patient's phenotype should be considered when evaluating them. It was also shown that PALB2, an established breast cancer susceptibility gene, indeed is definitively associated with breast cancer, and the NCGENES cancer patients have more truncating variants than the controls, further validating the clinical validity assertion. Finally, an ovarian cancer patient with two interesting variants, one in SLX4 and one in GEN1, were evaluated. Studies showed that knocking out both of these genes' pathways was highly destructive to the cell. A VUS was found in each of these genes, and it was hypothesized that perhaps these two variants together may be sufficient to contribute to this patient's cancer susceptibility.

Les obésités monogéniques et syndromiques sont des formes rares d'obésité, dont tous les facteurs génétiques ne sont pas connus. Quelle est l'implication des mutations du gène LEPR dans l'obésité sévère? Un séquençage de LEPR a été réalisé chez 535 sujets obèses Français.En France, les mutations homozygotes de LEPR ne sont pas rares (2,24%) et se caractérisent par une obésité extrême à début très précoce, troubles du comportement alimentaire et anomalies endocriniennes. En particulier, une nouvelle mutation ?exon6- 8 a été identifiée chez 6 sujets originaires de l'île de La Réunion, suggérant un effet isolat. La perte de poids après chirurgie bariatrique était très variable. Enfin, les sujets hétérozygotes ne présentaient pas de phénotype intermédiaire, avec une obésité inconstante sans anomalies endocriniennes. Quels sont les autres gènes impliqués dans les obésités syndromiques? Un séquençage d'exome a été réalisé chez 8 sujets avec obésité sévère et précoce et retard mental. Puis un variant a été génotypé chez 43 sujets atteints d'obésité syndromique, 178 ayant une obésité commune et 195 non obèses. Onze variants géniques ont été identifiés et étaient impliqués dans 4 voies physiopathologiques: neurogénèse, excitabilité neuronale/neurotransmission, remodelage de la chromatine, fonction ciliaire. Au vu de son potentiel effet délétère, un variant de MYT1L a été sélectionné et détecté chez 11,76% des patients ayant une obésité syndromique, 19,66% des enfants ayant une obésité commune et 6,67% des témoins suggérant un polymorphisme fréquent. Les sujets non porteurs avaient plus de probabilité d'avoir un IMC normal, suggérant le rôle de MYT1L dans le développement de l'obésité. / Monogenic and syndromic obesities are rare forms of obesity, which all genetic factors are not yet known.What is the implication of LEPR gene mutations in severe obesity?A direct sequencing of the LEPR gene was performed in 535 obese French subjects.In France, homozygous LEPR mutations are not rare (2.24%) and are characterized by extreme early-onset obesity, food impulsivity and endocrine disorders. Especially, we identified a new LEPR mutation Δexon6- 8 in 6 subjects originated from Reunion Island, suggesting a founder effect. Results concerning weight loss surgery were inconsistent in homozygous LEPR mutation carriers. Heterozygous LEPR mutation carriers exhibited no intermediate phenotype, with inconstant obesity and without endocrine abnormality. What are the other genes involved in syndromic obesities?A whole-exome sequencing was performed in 8 subjects with severe early-onset obesity and mental delay. Then a variant was genotyped in 43 subjects with syndromic obesity, 178 with common obesity and 195 nonobese controls.Eleven genic variants were identified and are implicated in 4 physiopathological pathways: neurogenesis, neuronal excitability/neurotransmission, chromatin remodelling, ciliary function. Because of its potential deleterious effect, a MYT1L variant was selected and detected in 11.76% of patients with syndromic obesity, 19.66% of children with common obesity, and 6.67% of controls, suggesting a common polymorphism. Non-carriers subjects had more probability to have a normal BMI, suggesting the role of MYT1L in obesity development.

During the Human Genome Project the first hundred billion bases were sequenced in four years, however, the second hundred billion bases were sequenced in four months (NHGRI, 2013). As efforts were made to improve every aspect of sequencing in this project, cost became inversely proportional to the speed (NHGRI, 2013). Human Genome Project ended in April 2003 but research in faster and cheaper ways to sequence the DNA is active to date (NHGRI, 2013). On the one hand, these advancements have allowed the convenient and unbiased generation and interrogation of a variety of omics datasets; on the other hand, they have substantially contributed towards the ever-increasing size of biological data. Therefore, informatics techniques are indispensable tools in the field of biology and medicine due to their ability to efficiently store and probe large datasets. Bioinformatics is a specialized domain under informatics that focusses on biological data storage, organization and analysis (NHGRI, 2013). Here, I have applied informatics approaches such as database designing and web development in the context of biological datasets or bioinformatics, to create a novel web-based resource that allows users to explore the comprehensive transcriptome of common aquatic tunicate named Oikopleura dioica (O .dioica), and access their associated annotations across key developmental time points, conveniently. This unique resource will substantially contribute towards studies on development, evolution and genetics of chordates using O. dioica as a model. Mendelian or single-gene disorders such as cystic fibrosis, sickle-cell anemia, Huntington’s disease, and Rett’s syndrome run across generations in families (Chial, 2008). Allelic variations associated with Mendelian disorders primarily reside in the protein-coding regions of the genome, collectively called an exome (Stenson et al., 2009). Therefore, sequencing of exome rather than whole genome is an efficient and practical approach to discover etiologic variants in our genome (Bamshad et al., 2011). Renal agenesis (RA) is a severe form of congenital anomalies of the kidney and urinary tract (CAKUT) where children are born with one (unilateral renal agenesis) or no kidneys (bilateral renal agenesis) (Brophy et al., 2017; Yalavarthy & Parikh, 2003). In this study, we have applied exome-sequencing technique to selective human patients in a renal agenesis (RA) pedigree that followed a Mendelian mode of disease transmission. Exome sequencing and molecular techniques combined with my bioinformatics analysis has led to the discovery of a novel RA gene called GREB1L (Brophy et al., 2017). In this study, we have successfully demonstrated the validation of exome sequencing and bioinformatics techniques to narrow down disease-associated mutations in human genome. Additionally, the results from this study has substantially contributed towards understanding the molecular basis of CAKUT. Discovery of novel etiologic variants will enhance our understanding of human diseases and development. High-throughput sequencing technique called RNA-Seq has revolutionized the field of transcriptome analysis (Z. Wang, Gerstein, & Snyder, 2009). Concisely, a library of cDNA is prepared from a RNA sample using an enzyme called reverse transcriptase (Nottingham et al., 2016). Next, the cDNA is fragmented, sequenced using a sequencing platform of choice and mapped to a reference genome, assembled transcriptome, or assembled de novo to generate a transcriptome (Grabherr et al., 2011; Nottingham et al., 2016). Mapping allows detection of high-resolution transcript boundaries, quantification of transcript expression and identification of novel transcripts in the genome. We have applied RNA-Seq to analyze the gene expression patterns in water flea otherwise known as D. pulex to work out the genetic details underlying heavy metal induced stress (unpublished) and predator induced phenotypic plasticity (PIPP) (Rozenberg et al., 2015), independently. My bioinformatics analysis of the RNA-Seq data has facilitated the discovery of key biological processes participating in metal induced stress response and predator induced defense mechanisms in D. pulex. These studies are great additions to the field of ecotoxicogenomics, phenotypic plasticity and have aided us in gaining mechanistic insight into the impact of toxicant and predator exposure on D. pulex at a bimolecular level.

Abstract Musculoskeletal diseases, such as osteoarthritis (OA), lumbar disc degeneration (LDD) and osteoporosis (OP), are common complex disorders affected by both environmental and genetic factors. OA and LDD are degenerative diseases affecting joints and spine and Modic changes (MC) are a specific phenotype of LDD. OP is a disorder causing bone fragility. There are families with a history of early onset cartilage degradation, disc disorders and bone fragility as well as rare, more severe disorders with these traits as part of the phenotype. The aim of this study was to identify predisposing genetic factors in Finnish families with three different musculoskeletal phenotypes and to investigate the use of whole exome sequencing (WES) as a tool. Six families were studied here, three diagnosed with hip and knee OA, two with MC and one with primary OP. Using WES together with in silico and in vitro analyses we identified new candidate genes. In the two OA families we identified family specific variants, c.-127G>T in the 5’UTR of FIP1L1 and p.Arg210Gly in OLIG3. We observed expression of these genes in human bone and cartilage. Both FIP1L1 and OLIG3 participate in the regulation of transcription. Family specific variants were also found in both families with MC: p.Gln1611fs in HSPG2 and p.Glu553Lys in MAML1. HSPG2 encodes for an important structural protein in the disc and MAML1 is a transcription factor. The family with primary OP had previously been reported to carry a heterozygous COL1A2 deletion leading to nonsense-mediated mRNA decay. In the WES we identified an additional change that may contribute to the phenotype: p.Arg428* in ZNF528. We showed experimentally that the variant leads to expression of a truncated form of ZNF528 in the nucleus. ZNF528 binding sites are located near genes associated with bone phenotypes. We identified twelve potential target genes for ZNF528 that were differentially expressed in patients’ cells compared to controls. Altogether, we identified five new candidate genes for the studied phenotypes demonstrating that WES can be used as a tool in studying complex musculoskeletal phenotypes in families. One of the identified candidate genes, HSPG2, encodes a structural protein, whereas, OLIG3, FIP1L1, MAML1 and ZNF528, participate in the regulation of transcription supporting the importance of regulatory mechanisms in the pathogenesis of musculoskeletal diseases. / Tiivistelmä Tuki- ja liikuntaelinsairaudet, kuten nivelrikko, välilevyrappeuma ja osteoporoosi, ovat yleisiä, monitekijäisiä sairauksia. Nivelrikko ja välilevynrappeuma ovat eteneviä nivelten ja selkärangan sairauksia. Modic muutokset ovat välilevyn ja nikaman välisten päätelevyjen muutoksia. Osteoporoosi on luuta haurastuttava sairaus. Varhaisessa iässä ilmenevää ruston haurastumista, välilevyn sairauksia tai luun haurautta tavataan myös suvuittain esiintyvinä sairauksina tai vakavien harvinaisten sairauksien oireina. Tutkimuksen tarkoitus oli tunnistaa altistavia geneettisiä tekijöitä kolmelle tuki- ja liikuntaelimistön sairaudelle suomalaisissa perheissä käyttäen eksomisekvensointi-menetelmää. Aineisto koostui kuudesta perheestä: kolmessa oli diagnosoitu lonkan ja polven nivelrikko, kahdessa selän välilevyjen Modic muutoksia ja yhdessä primaarinen vaikea selän osteoporoosi. Tunnistimme uusia ehdokasgeenejä käyttäen eksomisekvensointi-menetelmää sekä in silico ja in vitro analyysejä. Kahdessa nivelrikkoperheessä tunnistimme perhekohtaiset variantit kahdessa geenissä: c.-127G>T variantin FIP1L1 geenin säätelyalueella ja p.Arg210Gly variantin OLIG3 geenissä. Osoitimme, että nämä traskription säätelyyn osallistuvat geenit ilmenevät ihmisen luu- ja rustokudoksessa. Perhekohtaiset variantit havaittiin myös perheissä, joilla oli todettu Modic muutoksia: p.Gln1611fs HSPG2 -geenissä ja p.Glu553Lys MAML1 -geenissä. HSPG2 koodaa välilevylle tärkeää rakenneproteiinia ja MAML1 on transkriptiota säätelevä tekijä. Primaarista osteoporoosia sairastavalla perheellä oli aiemmin havaittu heterotsygootti, geenituotteen hajottamiseen johtava deleetio, COL1A2 -geenissä. Eksomisekvensoinnlla havaitsimme mahdollisesti taudin ilmiasuun lisäksi vaikuttavan muutoksen ZNF528 -geenissä. Osoitimme kokeellisesti, että havaittu variantti johtaa lyhentyneen proteiinin tuottoon solussa. ZNF528 on transkriptiotekijä, jolle tunnistimme kaksitoista mahdollista kohdegeeniä ja havaitsimme että niiden tuotto oli muuttunut potilaiden soluissa kontrollisoluihin verrattuna. Tunnistimme viisi uutta ehdokasgeeniä kolmessa eri sairaudessa eksomisekvensointi-menetelmän avulla. Yksi tunnistetuista geeneistä, HSPG2, koodaa rakenneproteiinia, ja muut osallistuvat transkription säätelyyn. Tämä tukee käsitystä säätelytekijöiden tärkeydestä TULE sairauksien synnyssä.

Family and twin studies have shown a heritable component to seasonal affective disorder (SAD). While a few studies have examined individual genetic variants in SAD, many methodological issues exist in the current literature. First, most studies combined major depression (MDD) and bipolar (BD) cases in the genetic analysis of SAD. This makes it difficult to differentiate the effect from MDD and BD. Second, most studies adopted a candidate gene approach and used fairly small sample sizes. This does not allow for testing across a wide variety of genes, and it yields less robust P-values. Third, healthy controls have been used, but not case comparisons, which makes it difficult to differentiate the effects of seasonality from that of the primary illness (MDD and BD). To overcome these issues, seasonal MDD and BD cases were separated into two different studies in this thesis; sample sizes for both studies are the largest in the current SAD molecular genetics literature; GWAS was used to test for potential risk loci in a hypothesis-free fashion; case comparisons were incorporated to exclude potential genetic contributions related generally to the primary diseases themselves (MDD and BD). For MDD, we performed a GWAS with 562 seasonal MDD cases and 1,225 comparison cases with non-seasonal MDD. Subjects were drawn from two iterations of the Genetics of Recurrent Early Onset Depression (GenRED) study. Seasonal cases were those whose depressive episodes typically started in fall or winter. A mega-analysis of the two GWAS datasets was done using SNPTEST. We found that two single nucleotide polymorphisms (SNPs), rs149882931 and rs77073398, on chromosome 16p12.1 were associated with seasonal depression, at a genome-wide significant level (OR= 1.66, P= 3.59 x 10-8 and OR=1.62, 4.76 x 10-8, respectively). Since SAD is more prevalent in females, a female-specific analysis was carried out. The two variants were more significant in this analysis: P=2.18x10-9 (OR=1.89) and P=2.79x10-9 (OR=1.82), respectively, and a significant sex-by-SNP interaction was observed. These SNPs are located in a conserved intergenic region between the genes HS3ST4 and C16orf82. The protein product of HS3ST4 modifies the side chains of heparan sulfate proteoglycans. We therefore tested the hypothesis that the heparan sulfate biosynthesis pathway would be enriched in nominally significant SNPs using the SNP ratio test, and found evidence for such enrichment (P=0.008, SNP ratio test, P=0.027, SKAT). For BD, the GWAS analysis of 818 seasonal BD cases and 1,515 healthy controls showed that BD-S is most strongly associated with two SNPs within the ZBTB20 genes. BD subjects were drawn from NIMH Bipolar Genetics Study (BIGS), and seasonal cases were defined as those with depressive episodes starting in fall or winter. An association study was carried out with SNPTEST, and we found two single nucleotide polymorphisms (SNPs) in the intronic region of ZBTB20 gene to be associated with BD-S (rs7646282, OR=2.34, P= 7.23 x 10-8 and rs139459337, OR=2.37, 8.05 x 10-8). A similar case-only study was carried out with 818 BD-S cases and 1239 cases without seasonal depressive symptoms (non-BDS), though no SNP was found to be significantly associated in this analysis. rs7646282 is the strongest SNP in cis-association with ZBTB20 gene expression, and ZBTB20 has been shown to affect the neural development of the hippocampus, a brain region implicated in the pathophysiology of BD. Finally, we sought to determine whether there is a role for circadian rhythm genes in BD susceptibility. In this study, we used a discovery set of 189 exome-sequenced BD patients and 105 healthy controls to look for circadian genes associated with BD. We found the DRD2 gene to be the circadian gene most strongly associated with BD. Among the rare damaging variants in the DRD2 gene, the S311C variant was the predominant SNP. To test whether this variant segregates in family members with BD, we genotyped the family members of probands from the discovery sample. This data was used for a linkage and family-based association study. Even though the linkage analysis was only very weakly positive, the family-based association study showed significant segregation of the variant in family members with BD (P< 0.05). To follow up on this finding, we further genotyped 2,185 unrelated BD cases and 1,982 healthy controls. We found no support for the S311C variant in this replication dataset. Sub-phenotype study of psychotic features and mood-incongruence also did not show significant association. Meta-analysis with 2,994 BD cases and 3,661 controls, however, revealed no association between the S311C variant and BD.

Abstract Undefined severe neurological and multi-organ diseases are rare as single diseases, but as a group of diseases, they are responsible for significant morbidity, impaired quality of life and mortality, emphasizing the importance of neuroscience research and its translation into novel diagnostic and treatment strategies. Molecular karyotyping and whole-exome sequencing were used to identify three novel disease-causing genes, GLE1, NHLRC2 and MYH7B, in Northem Finnish families having children with undefined progressive neuromuscular diseases. Functional studies on GLE1, NHLRC2, and MYH7B were conducted in order to understand better the impact of these mutations. The studies revealed that the cellular localization of GLE1 was impaired due to a mutation in the coding gene. The NHLRC2 is involved in many biological processes and its dysfunction has a role in the development of a novel FINCA disease and in fibrosis. Furthermore, mutations in MYH7B in the myosin family have now been connected to encephalomyopathies. Mutations in GLE1, NHLRC2 and MYH7B are involved in encephalomyopathies and neurodegeneration, stressing the important role of these genes in normal psychomotor development Analyses of these previously uncharacterized disease-causing gene mutations provided new insights into the etiologies behind these diseases, representing a relevant starting point for resolving the pathomechanisms underpinning these disorders. The newly-discovered human disease-causing genes and the novel phenotypes of childhood onset neuromuscular diseases provide the possibility for offering the relevant families preclinical diagnostics and may be beneficial in the identification of similar clinical phenotypes all around the world. / Tiivistelmä Yksittäiset, määrittelemättömät, vaikeat neurologiset monielinsairaudet ovat harvinaisia. Sen sijaan neurologisten ja monielinsairauksien alle ryhmittyvät taudit ovat merkittävä syy useisiin sairauksiin, jotka heikentävät elämänlaatua ja aiheuttavat kuolleisuutta. Tästä johtuen neurotieteiden tutkimus ja saatujen tulosten soveltaminen diagnostiikassa ja hoitomuotojen kehittämisessä on hyvin tärkeää. Molekyylikaryotyypitys- ja eksomisekvensointi-menetelmiä hyödynnettiin etsittäessä taudin syytä eteneville neuromuskulaarisairauksille pohjoissuomalaisissa perheissä. Tutkimuksessa tehtiin lisäksi funktionaalisia kokeita GLE1-, NHLRC2- ja MYH7B-proteiineilla, jotta ymmärrettäisiin paremmin löydettyjen mutaatioiden vaikutus potilaiden sairauksiin. Havaittiin, että GLE1-mutaatio vaikutti proteiinin solunsisäiseen paikantumiseen. NHLRC2-proteiini puolestaan on mukana useissa solun biologisissa prosesseissa ja sen toiminnanhäiriö vaikuttaa FINCA-taudin ja fibroosin kehittymiseen. MYH7B-myosiinigeenimutaatio puolestaan yhdistettiin ensimmäistä kertaa enkefalomyopatiaan. Havaittujen tautigeenien; GLE1, NHLRC2 ja MYH7B, vaikutus enkefalomyopatioissa ja neurodegeneraatiossa kertoo, että kyseisillä geeneillä on hyvin todennäköisesti tärkeä rooli ihmisen kehityksessä. Kyseisten, aiemmin tuntemattomien sairautta-aiheuttavien geenimutaatioiden analysointi lisäsi tietoa sairauksien etiologiasta ja loi pohjan tautimekanismien ratkaisemiselle tulevaisuudessa. Työssä esitettyjä uusia sairautta-aiheuttavia geenejä ja uusia karakterisoituja lapsuusiän neuromuskulaarisairauksien ilmiasuja voidaan hyödyntää perheille tarjotun sikiödiagnostiikan lisäksi myös muiden potilaiden samankaltaisen taudinkuvan diagnosoinnissa maailmanlaajuisesti.

Familial Pancreatic Cancer (FPC) is a cancer syndrome characterized by clustering of pancreatic cancer in families, but most FPC cases do not have a known genetic etiology. Understanding genetic predisposition to pancreatic cancer is important for improving screening as well as treatment. The central aim of this thesis is to identify candidate susceptibility genes for FPC, and I used three approaches of increasing resolution. First, based on a candidate-gene approach, I hypothesized that BRCA1 is inactivated by loss-of-heterozygosity in pancreatic adenocarcinoma of germline mutation carriers. I demonstrated that 5/7 pancreatic tumors from BRCA1-mutation carriers show LOH, compared to only 1/9 sporadic tumors, suggesting that BRCA1 inactivation is involved in tumorigenesis in germline mutation carriers. Second, I hypothesized that the germline genomes of FPC subjects differ in copy-number profile from healthy genomes, and that regions affected by rare deletions or duplications in FPC subjects overlap candidate tumor-suppressors or oncogenes. I found no significant difference in the global copy-number profile of FPC and control genomes, but I identified 93 copy-number variable genomic regions unique to FPC subjects, overlapping 88 genes of which several have functional roles in cancer development. I investigated one duplication to sequence the breakpoints, but I found that this duplication did not segregate with disease in the affected family. Third, I hypothesized that in a family with multiple pancreatic cancer patients, genes containing rare variants shared by the affected members constitute susceptibility genes. Using next-generation sequencing to capture most bases in coding regions of the genome, I interrogated the germline exome of three relatives who died of pancreatic cancer and a relative who is healthy at advanced age. I identified a short-list of nine candidate genes with unreported mutations shared by the three affected relatives and absent in the unaffected relative, of which a few had functional relevance to tumorigenesis. I performed Sanger sequencing to screen an unrelated cohort of approximately 70 FPC patients for mutations in the top two candidate genes, but I found no additional rare variants in those genes. In conclusion, I present a list of candidate FPC susceptibility genes for further validation and investigation in future studies.

Familial Pancreatic Cancer (FPC) is a cancer syndrome characterized by clustering of pancreatic cancer in families, but most FPC cases do not have a known genetic etiology. Understanding genetic predisposition to pancreatic cancer is important for improving screening as well as treatment. The central aim of this thesis is to identify candidate susceptibility genes for FPC, and I used three approaches of increasing resolution. First, based on a candidate-gene approach, I hypothesized that BRCA1 is inactivated by loss-of-heterozygosity in pancreatic adenocarcinoma of germline mutation carriers. I demonstrated that 5/7 pancreatic tumors from BRCA1-mutation carriers show LOH, compared to only 1/9 sporadic tumors, suggesting that BRCA1 inactivation is involved in tumorigenesis in germline mutation carriers. Second, I hypothesized that the germline genomes of FPC subjects differ in copy-number profile from healthy genomes, and that regions affected by rare deletions or duplications in FPC subjects overlap candidate tumor-suppressors or oncogenes. I found no significant difference in the global copy-number profile of FPC and control genomes, but I identified 93 copy-number variable genomic regions unique to FPC subjects, overlapping 88 genes of which several have functional roles in cancer development. I investigated one duplication to sequence the breakpoints, but I found that this duplication did not segregate with disease in the affected family. Third, I hypothesized that in a family with multiple pancreatic cancer patients, genes containing rare variants shared by the affected members constitute susceptibility genes. Using next-generation sequencing to capture most bases in coding regions of the genome, I interrogated the germline exome of three relatives who died of pancreatic cancer and a relative who is healthy at advanced age. I identified a short-list of nine candidate genes with unreported mutations shared by the three affected relatives and absent in the unaffected relative, of which a few had functional relevance to tumorigenesis. I performed Sanger sequencing to screen an unrelated cohort of approximately 70 FPC patients for mutations in the top two candidate genes, but I found no additional rare variants in those genes. In conclusion, I present a list of candidate FPC susceptibility genes for further validation and investigation in future studies.