Exome Sequencing Studies Research Articles

Finnish Parkinson\u2019s disease study integrating protein-protein interaction network data with exome sequencing analysis

Variants associated with Parkinson’s disease (PD) have generally a small effect size and, therefore, large sample sizes or targeted analyses are required to detect significant associations in a whole exome sequencing (WES) study. Here, we used protein-protein interaction (PPI) information on 36 genes with established or suggested associations with PD to target the analysis of the WES data. We performed an association analysis on WES data from 439 Finnish PD subjects and 855 controls, and included a Finnish population cohort as the replication dataset with 60 PD subjects and 8214 controls. Single variant association (SVA) test in the discovery dataset yielded 11 candidate variants in seven genes, but the associations were not significant in the replication cohort after correction for multiple testing. Polygenic risk score using variants rs2230288 and rs2291312, however, was associated to PD with odds ratio of 2.7 (95% confidence interval 1.4–5.2; p < 2.56e-03). Furthermore, an analysis of the PPI network revealed enriched clusters of biological processes among established and candidate genes, and these functional networks were visualized in the study. We identified novel candidate variants for PD using a gene prioritization based on PPI information, and described why these variants may be involved in the pathogenesis of PD.

Genepanel.iobio - an easy to use web tool for generating disease- and phenotype-associated gene lists

When ordering genetic testing or triaging candidate variants in exome and genome sequencing studies, it is critical to generate and test a comprehensive list of candidate genes that succinctly describe the complete and objective phenotypic features of disease. Significant efforts have been made to curate gene:disease associations both in academic research and commercial genetic testing laboratory settings. However, many of these valuable resources exist as islands and must be used independently, generating static, single-resource gene:disease association lists. Here we describe genepanel.iobio (https://genepanel.iobio.io) an easy to use, free and open-source web tool for generating disease- and phenotype-associated gene lists from multiple gene:disease association resources, including the NCBI Genetic Testing Registry (GTR), Phenolyzer, and the Human Phenotype Ontology (HPO). We demonstrate the utility of genepanel.iobio by applying it to complex, rare and undiagnosed disease cases that had reached a diagnostic conclusion. We find that genepanel.iobio is able to correctly prioritize the gene containing the diagnostic variant in roughly half of these challenging cases. Importantly, each component resource contributed diagnostic value, showing the benefits of this aggregate approach. We expect genepanel.iobio will improve the ease and diagnostic value of generating gene:disease association lists for genetic test ordering and whole genome or exome sequencing variant prioritization.

Exome sequencing study of Russian breast cancer patients suggests a predisposing role for USP39.

Germline variants in known breast cancer (BC) predisposing genes explain less than half of hereditary BC cases. This study aimed to identify missing genetic determinants of BC. Whole exome sequencing (WES) of lymphocyte DNA was performed for 49 Russian patients with clinical signs of genetic BC predisposition, who lacked Slavic founder mutations in BRCA1, BRCA2, CHEK2, and NBS1 genes. Bioinformatic analysis of WES data was allowed to compile a list of 229 candidate mutations. 79 of these mutations were subjected to a three-stage case-control analysis. The initial two stages, which involved up to 797 high-risk BC patients, 1504 consecutive BC cases, and 1081 healthy women, indicated a potentially BC-predisposing role for 6 candidates, i.e., USP39 c.*208G > C, PZP p.Arg680Ter, LEPREL1 p.Pro636Ser, SLIT3 p.Arg154Cys, CREB3 p.Lys157Glu, and ING1 p.Pro319Leu. USP39 c.*208G > C was strongly associated with triple-negative breast tumors (p = 0.0001). In the third replication stage, we genotyped the truncating variant of PZP (rs145240281) and the potential splice variant of USP39 (rs112653307) in three independent cohorts of Russian, Byelorussian, and German ancestry, comprising a total of 3216 cases and 2525 controls. The data obtained for USP39 rs112653307 supported the association identified in the initial stages (the combined OR 1.72, p = 0.035). This study suggests the role of a rare splicing variant in BC susceptibility. USP39 encodes an ubiquitin-specific peptidase that regulates cancer-relevant tumor suppressors including CHEK2. Further epidemiological and functional studies involving these gene variants are warranted.

Genomic Analysis of Hodgkin Lymphoma

The genetic analysis of the Hodgkin and Reed/Sternberg (HRS) tumor cells in Hodgkin lymphoma (HL) is very much hampered by the rarity of these cells, typically accounting for only about 1% of cells in the lymphoma tissue. Moreover, only very few cell lines were established from HL, partly with an uncertain origin. Thus, for the identification of somatic mutations in HRS cells, methods had to be established to isolate the rare HRS cells by microdissection from tissue sections or by cell sorting from cell suspensions. Initial studies were focussed on candidate gene approaches, often inspired by results from the prior analysis of HL cell lines. These early studies revealed numerous recurrent mutations in members of the NF-κB and JAK/STAT pathways, causing or at least contributing to the constitutive activation of these signaling pathways.1 The pathobiological relevance of the constitutive activation of NF-κB and JAK/STAT factors was validated by functional studies with HL cell lines. A first whole exome sequencing analysis of flow-sorted HRS cells was published by Reichel and colleagues.2 B2M was found to be inactivated by somatic mutations in 7/10 cases, and caused loss of major histocompatibility complex 1 expression. Although later studies with larger case series identified such mutations in only about 20-30% of cases,3,4 B2M inactivation is nevertheless an important factor for immune evasion of HRS cells and a frequently mutated gene in HL. A second exome sequencing study of HRS cells used microdissected tumor cells and revealed as a major novel finding frequent somatic mutations in the STAT6 gene (ca. 30% of cases).3 The genetic lesions in STAT6 are gain-of-function mutations. Overall nearly 90% of HL cases show genetic alterations in members of the JAK/STAT pathway, further demonstrating the major role of this pathway in HL pathogenesis. Our group is currently performing studies of microdissected HRS cells by whole genome sequencing, aiming to identify further genetic lesions in HRS cells beyond those affecting exons. An alternative attractive approach to uncover mutations in HRS cells is the genetic analysis of circulating DNA in plasma, because HRS cell-derived DNA fragments can be identified in most patients at the time of diagnosis. A targeted sequencing study of circulating tumor DNA showed the feasibility of this approach and validated, for example, the frequent occurrence of STAT6 mutations in HL. In rare instances, a HL can co-occur with another lymphoma in the same patient. Such composite lymphomas frequently show a common clonal origin of both lymphomas from a mature B cell.5 Composite lymphomas are therefore elegant models to study the multi-step transformation process in lymphomagenesis. We are currently performing a whole exome sequencing analysis of composite classical HL and B-cell Non-Hodgkin lymphomas, to reveal the pattern of early shared mutations and later distinct mutations. In each of the cases under investigations, such shared and distinct mutations were indeed identified. Küppers R, Engert A, Hansmann ML. Hodgkin lymphoma. J Clin Invest. 2012; 122: 3439. Reichel J, Chadburn A, Rubinstein PG, et al. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015; 125: 1061. Tiacci E, Ladewig E, Schiavoni G, et al. Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma. Blood. 2018; 131: 2454. Spina V, Bruscaggin A, Cuccaro A, et al. Circulating tumor DNA reveals genetics, clonal evolution, and residual disease in classical Hodgkinlymphoma. Blood. 2018; 131: 2413. Küppers R, Dührsen U, Hansmann ML. Pathogenesis, diagnosis, and treatment of composite lymphomas. Lancet Oncol. 2014; 15: e435. Disclosures No relevant conflicts of interest to declare.

Optimised molecular genetic diagnostics of Fanconi anaemia by whole exome sequencing and functional studies

PurposePatients with Fanconi anaemia (FA), a rare DNA repair genetic disease, exhibit chromosome fragility, bone marrow failure, malformations and cancer susceptibility. FA molecular diagnosis is challenging since FA is caused...

Exome sequencing study of partial agenesis of the corpus callosum in men with developmental delay, epilepsy, and microcephaly.

BackgroundThis study reports the genetic features of four Caucasian males from the Saguenay‒Lac‐St‐Jean region affected by partial agenesis of the corpus callosum (ACC) with hypotonia, epilepsy, developmental delay, microcephaly, hypoplasia, and autistic behavior.MethodsWe performed whole exome sequencing (WES) to identify new genes involved in this pathological phenotype. The regions of interest were subsequently sequenced for family members.ResultsSingle‐nucleotide variations (SNVs) and insertions or deletions were detected in genes potentially implicated in brain defects observed in these patients. One patient did not have mutations in genes related to ACC, but carried a de novo pathogenic mutation in Mucolipin‐1 (MCOLN1) and was diagnosed with mucolipidosis type IV. Among the other probands, missense SNVs were observed in DCLK2 (Doublecortin Like Kinase 2), HERC2 (HECT And RLD Domain Containing E3 Ubiquitin Protein Ligase 2), and KCNH3 (Potassium channel, voltage‐gated, subfamily H, member 3). One patient also carried a non‐frameshift insertion in CACNA1A (Cav2.1(P/Q‐type) calcium channels).ConclusionAlthough no common genetic defect was observed in this study, we provide evidence for new avenues of investigation for ACC, such as molecular pathways involving HERC2, CACNA1A, KCNH3, and more importantly DCLK2. We also allowed to diagnose an individual with mucolipidosis type IV.

Novel Targeted Therapies in Uterine Carcinosarcomas

Abstract Uterine Carcinosarcomas (UCSs) in gynecology are very infrequent and represent only 2-5% of uterine cancers. Despite surgical cytoreduction and subsequent chemotherapy being the primary treatment for UCSs, the overall five-year survival rate is 30% and recurrence is extremely common (50-80%). UCSs are also aggressive tumors previously considered to be sarcomas, but now recognized as malignancies composed of metaplastic transformation of epithelial elements. Much of the management for UCS has been extrapolated from studies of endometrial carcinomas and sarcomas. The development of novel, effective treatment strategies against UCSs of the female genital tract remains an unmet medical need. Whole exome sequencing studies have recently demonstrated mutations or aberrant activation of multiple genes/pathways in UCSs including HER2 (Human Epidermal Growth Factor Receptor 2), PI3K (phosphatidylinositol-3 kinase)/AKT/mTOR (mammallian target of rapamycin), EGFR (Epidermal Growth Factor Receptor), MARK (mitogen-activated protein kinase), genes related to histones and chromatin structure, and genes related to cell-cycle regulation. The carcinomatous component of these biphasic tumors is suggested to be the catalyst in UCSs tumorigenesis. New strategies have been developed in the last few decades, targeting known dysfunctional molecular pathways for immunotherapy. This session reviews the genetic landscapes and explores novel targeted treatment modalities against this deadly gynecologic tumor.

Clinical features and genetic characteristics of myoclonic-atonic epilepsy caused by SLC6A1 gene mutation

Objective To explore the clinical features and genetic characteristics of myoclonic-atonic (MAE) caused by gene mutation. Methods The clinical data of a patient with gene mutation from Xiangya Hospital of Central South University was collected. The related literatures were reviewed from Wanfang Data, China National Knowledge Infrastructure, PubMed (until July 2019) by using keywords SLC6A1 and myoclonic-atonic epilepsy . The characteristics of gene mutation and the clinical phenotype of children with myoclonic-atonic were summarized. Results A 8 year and 8 months old girl was enrolled in the study. Her first attack happened at the age of 19 months, and multiple seizure types including myoclonic-atonic, atonic and absence were observed. The seizures were well controlled by valproate (VPA), but she has mild-moderate intellectual disability. Whole exome-sequencing study identified a de novo nonsense variant of c. 46G>T(p.Glu16*)in gene. A total of 27 cases including the present case with gene mutation were analyzed. 22 mutations were identified, including 11 missense mutations, 5 nonsense mutations, 3 frameshift mutations, 2 splicing mutation and 1 with chromosome microdeletion. Among them 26 patients had more one type of seizures, 20 cases had absence seizures, 17 cases had atonic seizures, 14 cases had myoclonic seizures, 11 cases had myoclonic-atonic seizures, 4 cases had generalized tonic-clonic seizures, 3 cases had eyelid myoclonias, 2 cases had nonconvulsive status epilepticus and 2 cases had tonic seizure. 24 patients had described intelligence assessment. Among them, 18 had developmental delay before onset, 11 had developmental regression after onset. There were 9 cases with autistic features, 4 cases with attention deficit hyperactivity disorder and 3 cases with ataxia. The seizures of 17 cases were controlled, 4 cases had partial seizure control, 3 cases had no significant improvement, and other 3 cases were unclear. Conclusions The main clinical feature of MAE patients with gene mutations is absence and atonic seizures, cognition before onset can be impaired, and some patients had behavioral problems, such as autistic features or attention deficit hyperactivity disorders. VPA is recommend as first-line treatment. Key words: Epilepsies, myoclonic; Epilepsy, absence; Glucose transporter type 1; Mutation; Child

Characterization of intellectual disability and autism comorbidity through gene panel sequencing.

Intellectual disability (ID) and autism spectrum disorder (ASD) are clinically and genetically heterogeneous diseases. Recent whole exome sequencing studies indicated that genes associated with different neurological diseases are shared across disorders and converge on common functional pathways. Using the Ion Torrent platform, we developed a low-cost next-generation sequencing gene panel that has been transferred into clinical practice, replacing single disease-gene analyses for the early diagnosis of individuals with ID/ASD. The gene panel was designed using an innovative in silico approach based on disease networks and mining data from public resources to score disease-gene associations. We analyzed 150 unrelated individuals with ID and/or ASD and a confident diagnosis has been reached in 26 cases (17%). Likely pathogenic mutations have been identified in another 15 patients, reaching a total diagnostic yield of 27%. Our data also support the pathogenic role of genes recently proposed to be involved in ASD. Although many of the identified variants need further investigation to be considered disease-causing, our results indicate the efficiency of the targeted gene panel on the identification of novel and rare variants in patients with ID and ASD.

Elucidation of the phenotypic spectrum and genetic landscape in primary and secondary microcephaly

PurposeMicrocephaly is a sign of many genetic conditions but has been rarely systematically evaluated. We therefore comprehensively studied the clinical and genetic landscape of an unselected cohort of patients with microcephaly. MethodsWe performed clinical assessment, high-resolution chromosomal microarray analysis, exome sequencing, and functional studies in 62 patients (58% with primary microcephaly [PM], 27% with secondary microcephaly [SM], and 15% of unknown onset). ResultsWe found severity of developmental delay/intellectual disability correlating with severity of microcephaly in PM, but not SM. We detected causative variants in 48.4% of patients and found divergent inheritance and variant pattern for PM (mainly recessive and likely gene-disrupting [LGD]) versus SM (all dominant de novo and evenly LGD or missense). While centrosome-related pathways were solely identified in PM, transcriptional regulation was the most frequently affected pathway in both SM and PM. Unexpectedly, we found causative variants in different mitochondria-related genes accounting for ~5% of patients, which emphasizes their role even in syndromic PM. Additionally, we delineated novel candidate genes involved in centrosome-related pathway (SPAG5, TEDC1), Wnt signaling (VPS26A, ZNRF3), and RNA trafficking (DDX1). ConclusionOur findings enable improved evaluation and genetic counseling of PM and SM patients and further elucidate microcephaly pathways.

Molecular characterization of acute myeloid leukemia patients who relapse more than 3 years after diagnosis: an exome sequencing study of 31 patients

Acute myeloid leukemia (AML) is the most common acute leukemia in adults, with affected patients having a median age of 65-70 years at diagnosis. Standard chemotherapy protocols result in remission in ~40-80% of patients. Relapse of the disease, however, is common and associated with a dismal

Exome sequencing of Finnish isolates enhances rare-variant association power.

Exome sequencing studies have generally been underpowered to identify deleterious alleles with a large effect on complex traits, as such alleles are mostly rare. Because the population of northern and eastern Finland has expanded dramatically and in isolation following a series of bottlenecks, it harbors numerous deleterious alleles at relatively high frequency. Capitalizing on this circumstance, we exome sequenced nearly 20,000 individuals from these regions. Exome-wide association studies for 64 quantitative traits clinically relevant to cardiovascular and metabolic disease identified 26 newly associated deleterious alleles. Nineteen of these alleles are either unique to or >20 times more frequent in Finns than in other Europeans and show geographical clustering comparable to Mendelian disease mutations characteristic of the Finnish population. We estimate that sequencing studies in populations without this unique history would require hundreds of thousands to millions of participants to achieve comparable association power.

Systematic Review of Somatic Mutations in Splenic Marginal Zone Lymphoma

The aims of this systematic review are to refine the catalogue of somatic variants in splenic marginal zone lymphoma (SMZL) and to provide a well-annotated, manually curated database of high-confidence somatic mutations to facilitate variant interpretation for further biological studies and future clinical implementation. Two independent reviewers systematically searched PubMed and Ovid in January 2019 and included studies that sequenced SMZL cases with confirmed diagnosis. The database included fourteen studies, comprising 2817 variants in over 1000 genes from 475 cases. We confirmed the high prevalence of NOTCH2, KLF2 and TP53 mutations and analysis of targeted genes further implicated TNFAIP3, KMT2D, and TRAF3 as recurrent targets of somatic mutation based on their high incidence across studies. The major limitations we encountered were the low number of patients with whole-genome, unbiased analysis and the relative sensitivities of differing sequencing approaches. Overall, we showed that there is little concordance between whole exome sequencing studies of SMZL. We strongly support the continuing unbiased analysis of the SMZL genome for mutations in all protein-coding genes and provide a valuable database resource to facilitate this endeavour that will ultimately improve our understanding of SMZL pathobiology.

Development of anthracycline-induced dilated cardiomyopathy due to mutation on LMNA gene in a breast cancer patient: a case report

BackgroundAnthracyclines are highly effective anticancer medication prescribed for the treatment of breast cancer. Nevertheless, the use of anthracyclines as chemotherapeutic agents involves a risk for development of cardiac toxicity which may cause restrictive and dilated cardiomyopathy. Currently, genetic predisposition is not considered as a risk factor for cardiotoxicity associated to the use of anthracyclines.Case presentationWe report the case of a 37-years old Panamanian female patient diagnosed with breast cancer who developed clinical signs of severe heart failure after treatment with doxorubicin. A diagnosis of anthracycline induced cardiomyopathy was made and treatment was initiated accordingly. A whole exome sequencing study performed to the patient showed the presence of a missense mutation in LMNA gene, which codifies for lamin A/C. Our results points to a correlation between the LMNA variant and the anthracycline cardiotoxicity developed by the woman. Improvement of the clinical symptoms and the left ventricle ejection fraction was observed after proper treatment.ConclusionsThis case report suggests for the first time a potential genetic predisposition for anthracyclines induced cardiomyopathy in patients with mutations in LMNA gene. Perhaps chemotherapies accelerate or deliver the “second-hit” in the development of DCM in patients with genetic mutations. More data is needed to understand the contribution of LMNA variants that predispose to DCM in patients receiving cardiotoxic therapies.

Whole exome sequencing study of a Chinese concurrent cancer family.

Cancer is one of the leading causes of mortality in China, and poses a threat to public health due to its increasing incidence and mortality rates. Concurrent cancer is defined as one or more organs in the same individual having ≥2 primary malignancies occurring simultaneously or successively; however, concurrent cases are rare and poorly studied. The present study recruited a Chinese family presenting multiple cases of concurrent cancer and performed whole exome sequencing in one unaffected and two affected individuals to identify the causative mutations. DNA was extracted from peripheral blood and tumor tissue samples. Following an exome capture and quality test, the qualified library was sequenced as 100 bp paired-end reads on an Ion Torrent platform. Clean data were obtained by filtering out the low-quality reads. Subsequently, bioinformatics analyses were performed using the clean data. After mapping and annotating in 1000 Genomes Project database, the existing SNP database and the Cancer Gene Census (CGC) database, it was revealed that the NADH:ubiquinone oxidoreductase core subunit S7 gene was a candidate gene with somatic mutations, and a subset of 16 genes were candidate genes with germline mutations. The findings of the present study may improve the understanding of the molecular pathogenesis of concurrent cancer.

Abstract LB-180: Underreporting of race in genomic sequencing studies increases cancer health information disparities

Abstract Purpose: Minorities are often underrepresented in clinical cancer research and the frequency of reporting of race in genomic sequencing studies of cancer is unknown. Disproportionate reporting of race can widen health information disparities and impair clinical decision-making in the underrepresented minority populations in whom cancer disease burden is greatest. This study determined the extent to which race is reported as a clinical variable in sequencing studies of cancer in the United States, the factors associated with reporting of race, and the participation rates of minority populations. Methods: PubMed was systematically searched from January 1, 2010 through November 15, 2018 and a total of 9,410 non-duplicated studies were assessed for eligibility. Publications reporting whole genome or exome sequencing data for patients with one of the ten most common cancers in the United States at sufficient depth to identify rare variants were included in this study. Results: 234 publications containing sequencing data from 16,358 unique patients met inclusion criteria. 36% of studies reported race as a clinical variable compared to 84% of studies reporting age and 83% of studies reporting gender. Reporting of race was associated with cancer type, cohort size, sequencing method, and tissue acquisition date. Minority populations were significantly underpowered to detect recurrent mutations in the majority of cancer types due to small sample size. Conclusion: Race is underreported as a clinical variable in whole genome and exome sequencing studies of cancer in the United States. As the patient populations represented in research studies directly inform clinical decision-making and outcomes, substantially increased efforts are needed to sequence patients from underrepresented populations in order to reduce health disparities in patients of non-European ancestry. Citation Format: Adrienne Nugent, Kelly R. Conatser, Llaran L. Turner, James T. Nugent, Esther May Sarino, Luisel J. Ricks-Santi. Underreporting of race in genomic sequencing studies increases cancer health information disparities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-180.

Abstract 174: Functional characterization of ZNF750 in esophageal squamous cell carcinoma

Abstract Background: Esophageal squamous cell carcinoma (ESCC) is a lethal and aggressive malignancy that is a threat worldwide. It is of significant prevalence in regions of Asia including Iran, Korea, Japan and especially China. Epidemiological studies of ESCC reveal genetic variations as a risk-factor to ESCC incidence. Genomic profiling of ESCC primary tumors have already identified candidate genes involved in different cellular processes such as cell cycle and apoptosis. Data from our whole exome sequencing study of primary tumors and lymph node metastases also reveal mutations involved in these pathways; however, we also uncovered an interesting candidate involved in differentiation namely, ZNF750. ZNF750 has been reported to play important roles in other squamous cell carcinomas, and as a candidate tumor suppressor gene in ESCC. Methods and Results: We exogenously upregulated ZNF750 expression by lentiviral system and used this model to investigate ZNF750 function in ESCC. By MTT 2D cell proliferation assay, we showed that in vitro cell proliferation in the ZNF750 group was hindered compared to controls. In addition, we set up 2D and 3D colony formation assays and found that the ZNF750 groups produced fewer colonies in 2D culture plates and produced significantly smaller colonies, when embedded in Matrigel. All of these findings are consistent with previous studies. We also studied the potential functional role of ZNF750 in 3D invasion/migration. Transwell permeable inserts were used to support a thick Matrigel culture with a nutrient gradient. Cells were embedded in Matrigel and moved along the gradient within the gel. After prolonged incubation (&amp;gt;2 weeks), location and size of the colonies were examined by confocal microscopy scanning. Cells with upregulated ZNF750 were found to exhibit greater mobility compared to the control cells. We also subjected ZNF750 and control groups to cisplatin to test for chemoresistance in ESCC. We found that ZNF750 expression increases chemoresistance, as opposed to the control cells. Conclusion: From these results, ZNF750 expression inhibits cell proliferation, while enhancing cell mobility and drug resistance, all of which are characteristics of cells undergoing epithelial-mesenchymal transition (EMT). We, therefore, hypothesize that ZNF750 functions in ESSC beyond that of a tumor suppressor, but as a putative EMT regulator. Acknowledgements: Research Grants Council Collaborative Research Fund grant number 106150246 and Asian Cancer Research Fund to MLL. Citation Format: Sheyne SA Choi, Valen Zhuoyou Yu, Josephine Mun-Yee Ko, Wei Dai, Maria L. Lung. Functional characterization of ZNF750 in esophageal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 174.

Whole exome sequencing of patients who resolved Crohn\u2019s disease and complex regional pain syndrome following treatment for paratuberculosis

BackgroundA whole exome sequencing study was performed on an extended family including a patient with Crohn’s disease (CD) and a patient with complex regional pain syndrome (CRPS). The patient with CD and the patient with CRPS have experienced resolution of their disease following treatment for paratuberculosis. The study was performed in order to determine if there is an unusual mutation in this extended family that would explain the susceptibility to mycobacterial infection among many of the members.ResultsWe identified sets of rare single nucleotide polymorphisms (SNPs) that were shared among affected family members, including variants in two genes, IL15RA and CASP10, which have established roles in the immune response. In addition, the CD and CRPS patients were found to have heterozygous mutations in MBL2 and DDX58, mutations that have been associated with susceptibility to tuberculosis.ConclusionsThe IL15RA and CASP10 variants may contribute to the disease symptoms exhibited in this family. The finding of SNPs associated with immune function supports a complementary role of infection and genetics in these diseases.

Whole exome sequencing detects novel variants in Saudi children diagnosed with eczema

BackgroundEczema is also known as atopic dermatitis is well-known for the skin disease globally. In Saudi Arabia, exome sequencing studies have not been documented. The purpose of this study was to scrutinize the disease causing mutations in children affected with eczema with exome sequencing in the Saudi population. MethodsWe recruited randomly three sporadic cases of children diagnosed with eczema and simultaneously, three more cases were adopted for control samples. Exome sequencing was carried out by applying a pipeline that captures all the variants of concern related to the samples by using the Ion torrent. ResultsIn this study, we have documented 49 variants, among which 37 variants were confirmed through eczema children and remaining 30 variants through control children. However, from the analysis of the 6 samples, we have identified rs10192157 (1646C>T; Thr549Ile), rs2899642 (27C>G; Asn9Lys), chr1:152127950 (1625G>A; Gly542Asp) and chr1:152128041 (1534C>G; Gly512Arg) variants which are rarely linked to the disease eczema. In the rs10192157, we have documented these mutations in all three eczema children and one in the control; the rs2899642 mutation appeared in only a couple of eczema children, whereas the mutation in the chr1:152127950 regions appeared in only one eczema patient. However, the chr1:152128041 mutations appeared in only one case of eczema and also in two control children. ConclusionOur study revealed four mutations which had not previously been connected with eczema within the database. However, the rs10192157 and rs2899642 mutations were documented with asthma disease. The remaining mutations such as chr1:152127950 and chr1:152128041 have not been reported anywhere else. This study recommends screening these 4 mutations in eczema cases and their relevant controls to confirm the prevalence in the Saudi population. It is recommended that future studies examine the 4 mutations in detail.

S119 THE ROLE OF RECURRENT SOMATIC ALTERATIONS IN THE NON-CODING GENOME WITH FUNCTIONAL IMPLICATIONS IN MM

Background: Multiple Myeloma (MM) is a heterogenous disease with distinct molecular and clinical characteristics. Recent large collaborative efforts have identified number of driver genes. However over 96% of all somatic alterations occur in non-coding regions and very little is known about how they affect the disease. Aims: Using our large dataset from uniformly treated newly diagnosed patinets as well as relpased patient samples, we investigated the somatic alterations in the non coding genome to identify critical hotspots. Methods: We performed a deep (average coverage > 80X) whole genome sequencing (WGS) on 376 MM samples (240 newly diagnosed, 52 first relapse and 84 rrMM) as well as RNAseq to comprehensively analyze recurrent somatic alterations in non-coding regions. Results: We detected median 9,649 (Range 3,194–126,935) mutations and indels per sample with overall more than 4 M total somatic mutations. Introns (> 2.5 mutations/per Mb) and intergenic regions (> 3 mutations/per Mb) had significantly higher number of mutations per megabase compared to Exons (∼2 mutations/per Mb) (p < 1e-5). Mutations in coding regions in our data was similar to published whole exome sequencing studies with increase in several driver mutations at relapse. We observed 57 [range 7 - 376] structural variants (SVs) per sample with > 98% involving non-coding regions. We identified 48 SV hotspots that are targeting tumor suppressor genes or key regulatory elements such as TCF3 and TNFSF10 and these SVs were also associated with significantly altered expression of the target genes. We have detected two less defined translocations targeting MAP3K14 and NFKB1 and driving the expressions of these genes. Our data showed that ∼80% of translocation breakpoints are in the close proximity of super enhancers and therefore Ig is not the only mechanism over expresses the target genes. We detected >500 single nucleotide hotspots in the con-coding genome some of which are targeting 5’UTR and introns of BCL7A, BCL6, CD93, CCND1, PAX5. Some of these hotspots were correlated with disease outcome. We also observed that overall mutational load is also associated with disease outcome. We detected chromothripsis in ∼25% of newly diagnosed samples; and kataegis hotspots on chromosome 3q27-3q28 (24%), 11q13 (5.8%) and 12q24 (5.3%). Summary/Conclusion: In conclusion, this large deep whole genome sequencing data from newly-diagnosed MM patients identifies a vast majority of non-coding mutations with potentially significant functional and biological role in MM. Our integrative approach using both WGS and RNA-seq data from the patients now provides us important tools to further characterize the impact of these mutations and develop opportunities for targeted therapeutics.