Whole Genome Sequencing Prioritizes CHEK2, EWSR1, and TIAM1 as Possible Predisposition Genes for Familial Non-Medullary Thyroid Cancer

Familial inheritance in non-medullary thyroid cancer (NMTC) is an area that has yet to be adequately explored. Despite evidence suggesting strong familial clustering of non-syndromic NMTC, known variants still account for a very small percentage of the genetic burden. In a recent whole genome sequencing (WGS) study of five families with several NMTCs, we shortlisted promising variants with the help of our in-house developed Familial Cancer Variant Prioritization Pipeline (FCVPPv2). Here, we report potentially disease-causing variants in checkpoint kinase 2 (CHEK2), Ewing sarcoma breakpoint region 1 (EWSR1) and T-lymphoma invasion and metastasis-inducing protein 1 (TIAM1) in one family. Performing WGS on three cases, one probable case and one healthy individual in a family with familial NMTC left us with 112254 variants with a minor allele frequency of less than 0.1%, which was reduced by pedigree-based filtering to 6368. Application of the pipeline led to the prioritization of seven coding and nine non-coding variants from this family. The variant identified in CHEK2, a known tumor suppressor gene involved in DNA damage-induced DNA repair, cell cycle arrest, and apoptosis, has been previously identified as a germline variant in breast and prostate cancer and has been functionally validated by Roeb et al. in a yeast-based assay to have an intermediate effect on protein function. We thus hypothesized that this family may harbor additional disease-causing variants in other functionally related genes. We evaluated two further variants in EWSR1 and TIAM1 with promising in silico results and reported interaction in the DNA-damage repair pathway. Hence, we propose a polygenic mode of inheritance in this family. As familial NMTC is considered to be more aggressive than its sporadic counterpart, it is important to identify such susceptibility genes and their associated pathways. In this way, the advancement of personalized medicine in NMTC patients can be fostered. We also wish to reopen the discussion on monogenic vs polygenic inheritance in NMTC and instigate further development in this area of research.

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Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways

Biomolecules ◽

10.3390/biom9100605 ◽

2019 ◽

Vol 9 (10) ◽

pp. 605 ◽

Cited By ~ 5

Author(s):

Aayushi Srivastava ◽

Abhishek Kumar ◽

Sara Giangiobbe ◽

Elena Bonora ◽

Kari Hemminki ◽

...

Keyword(s):

Thyroid Cancer ◽

Whole Genome Sequencing ◽

Signaling Pathways ◽

Genome Sequencing ◽

Tyrosine Kinases ◽

Medullary Thyroid Cancer ◽

Familial Cancer ◽

Whole Genome ◽

Medullary Thyroid ◽

Genetic Burden

Evidence of familial inheritance in non-medullary thyroid cancer (NMTC) has accumulated over the last few decades. However, known variants account for a very small percentage of the genetic burden. Here, we focused on the identification of common pathways and networks enriched in NMTC families to better understand its pathogenesis with the final aim of identifying one novel high/moderate-penetrance germline predisposition variant segregating with the disease in each studied family. We performed whole genome sequencing on 23 affected and 3 unaffected family members from five NMTC-prone families and prioritized the identified variants using our Familial Cancer Variant Prioritization Pipeline (FCVPPv2). In total, 31 coding variants and 39 variants located in upstream, downstream, 5′ or 3′ untranslated regions passed FCVPPv2 filtering. Altogether, 210 genes affected by variants that passed the first three steps of the FCVPPv2 were analyzed using Ingenuity Pathway Analysis software. These genes were enriched in tumorigenic signaling pathways mediated by receptor tyrosine kinases and G-protein coupled receptors, implicating a central role of PI3K/AKT and MAPK/ERK signaling in familial NMTC. Our approach can facilitate the identification and functional validation of causal variants in each family as well as the screening and genetic counseling of other individuals at risk of developing NMTC.

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Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways

10.20944/preprints201910.0154.v1 ◽

2019 ◽

Cited By ~ 1

Author(s):

Aayushi Srivastava ◽

Abhishek Kumar ◽

Sara Giangiobbe ◽

Elena Bonora ◽

Kari Hemminki ◽

...

Keyword(s):

Thyroid Cancer ◽

Whole Genome Sequencing ◽

Signaling Pathways ◽

Genome Sequencing ◽

Tyrosine Kinases ◽

Medullary Thyroid Cancer ◽

Familial Cancer ◽

Whole Genome ◽

Medullary Thyroid ◽

Genetic Burden

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Whole‐genome sequencing of synchronous thyroid carcinomas identifies aberrant DNA repair in thyroid cancer dedifferentiation

The Journal of Pathology ◽

10.1002/path.5359 ◽

2019 ◽

Vol 250 (2) ◽

pp. 183-194 ◽

Cited By ~ 8

Author(s):

Johan O Paulsson ◽

Samuel Backman ◽

Na Wang ◽

Adam Stenman ◽

Joakim Crona ◽

...

Keyword(s):

Dna Repair ◽

Thyroid Cancer ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Thyroid Carcinomas

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Determinants of spontaneous mutation in the bacteriumEscherichia colias revealed by whole-genome sequencing

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1512136112 ◽

2015 ◽

Vol 112 (44) ◽

pp. E5990-E5999 ◽

Cited By ~ 64

Author(s):

Patricia L. Foster ◽

Heewook Lee ◽

Ellen Popodi ◽

Jesse P. Townes ◽

Haixu Tang

Keyword(s):

Dna Damage ◽

Oxidative Damage ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Oxidative Dna Damage ◽

Spontaneous Mutation ◽

Mutation Rates ◽

Whole Genome ◽

Entire Genome ◽

Local Sequence

A complete understanding of evolutionary processes requires that factors determining spontaneous mutation rates and spectra be identified and characterized. Using mutation accumulation followed by whole-genome sequencing, we found that the mutation rates of three widely diverged commensalEscherichia colistrains differ only by about 50%, suggesting that a rate of 1–2 × 10−3mutations per generation per genome is common for this bacterium. Four major forces are postulated to contribute to spontaneous mutations: intrinsic DNA polymerase errors, endogenously induced DNA damage, DNA damage caused by exogenous agents, and the activities of error-prone polymerases. To determine the relative importance of these factors, we studied 11 strains, each defective for a major DNA repair pathway. The striking result was that only loss of the ability to prevent or repair oxidative DNA damage significantly impacted mutation rates or spectra. These results suggest that, with the exception of oxidative damage, endogenously induced DNA damage does not perturb the overall accuracy of DNA replication in normally growing cells and that repair pathways may exist primarily to defend against exogenously induced DNA damage. The thousands of mutations caused by oxidative damage recovered across the entire genome revealed strong local-sequence biases of these mutations. Specifically, we found that the identity of the 3′ base can affect the mutability of a purine by oxidative damage by as much as eightfold.

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Identification of Familial Hodgkin Lymphoma Predisposing Genes Using Whole Genome Sequencing

10.1101/2019.12.12.19014324 ◽

2019 ◽

Author(s):

Aayushi Srivastava ◽

Sara Giangiobbe ◽

Abhishek Kumar ◽

Dagmara Dymerska ◽

Wolfgang Behnisch ◽

...

Keyword(s):

B Cell ◽

Whole Genome Sequencing ◽

Hodgkin Lymphoma ◽

Genome Sequencing ◽

Pathway Analysis ◽

Cell Activation ◽

Familial Cancer ◽

Amino Acid Sequences ◽

Clear Understanding ◽

Whole Genome

AbstractHodgkin lymphoma (HL) is a lymphoproliferative malignancy of B-cell origin that accounts for 10% of all lymphomas. Despite evidence suggesting strong familial clustering of HL, there is no clear understanding of the contribution of genes predisposing to HL. In this study, whole genome sequencing (WGS) was performed on 7 affected and 9 unaffected family members from three HL-prone families and variants were prioritized using our Familial Cancer Variant Prioritization Pipeline (FCVPPv2). WGS identified a total of 98564, 170550 and 113654 variants which were reduced by pedigree-based filtering to 18158, 465 and 26465 in families I, II and III, respectively. In addition to variants affecting amino acid sequences, variants in promoters, enhancers, transcription factors binding sites and microRNA seed sequences were identified from upstream, downstream, 5’ and 3’ untranslated regions. A panel of 565 cancer predisposing and other cancer-related genes and of 2383 high-risk HL genes were also screened in these families to aid further prioritization. Pathway analysis of segregating genes with CADD (Combined Annotation Dependent Depletion Tool) scores > 20 was performed using Ingenuity Pathway Analysis software which implicated several candidate genes in pathways involved in B-cell activation and proliferation and in the network of “Cancer, Hematological disease and Immunological Disease”. We used the FCVPPv2 for further in silico analysis and prioritized 45 coding and 79 non-coding variants from the three families. Further literature-based analysis allowed us to constrict this list to one rare germline variant each in families I and II and two in family III. Functional studies were conducted on the candidate from family I in a previous study, resulting in the identification and functional validation of a novel heterozygous missense variant in the tumor suppressor gene DICER1 as potential HL predisposition factor. We aim to identify the individual genes responsible for predisposition in the remaining two families and will functionally validate these in further studies.

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Whole Genome Sequencing Uncovers a Rare Germline Variant in ATM Associated with Familial Myeloproliferative Neoplasms

Blood ◽

10.1182/blood-2021-153317 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 3592-3592

Author(s):

Shiyu Wang ◽

Hang Chen ◽

Eddie Imada ◽

Jack Ghannam ◽

Clifton L. Dalgard ◽

...

Keyword(s):

Dna Damage ◽

General Population ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Myeloproliferative Neoplasms ◽

Study Cohort ◽

Whole Genome ◽

Germline Variant ◽

Damage Repair ◽

Familial Clustering

Abstract Introduction: Myeloproliferative neoplasms (MPN) are sporadic diseases characterized by a somatic driver mutation in the JAK2, CALR or MPL gene. Although it is generally considered a sporadic disease, approximately 10% of MPN cases display familial clustering, and there is a 5 to 7-fold increased risk of developing an MPN among first degree relatives of MPN patients. In contrast to other myeloid malignancies, investigation of large pedigrees with familial clustering of MPN has failed to identify high-risk predisposition genes relevant to the general MPN population. Genome wide association studies (GWAS) have identified common, low penetrance risk alleles for MPN predisposition in multiple genes including JAK2, TERT, TET2, ATM and SH2B3. In order to identify novel germline predisposition variants in MPN, an unbiased whole genome sequencing (WGS) approach was utilized to examine genomic structure and germline variations in a cohort of individuals with familial MPN. Methods: The study cohort was comprised of 67 individuals with familial MPN enrolled in a prospective research registry at Johns Hopkins Hospital. Familial MPN was defined as a diagnosis of MPN in an individual with a family history of MPN or related myeloid malignancy (myelodysplastic syndrome and chronic myelomonocytic leukemia) in a first or second degree relative. Neutrophil genomic DNA was subjected to WGS using Illumina HiSeq platform and sequenced to 60x depth. We performed germline variant calling using HaplotypeCaller and following the GATK best practices. The variants detected were further enriched for germline by allele frequency 40-60% or >90% and presence in the gnomAD database. Non-synonymous coding variants that occurred in the study cohort at a statistically higher frequency that in the general population (gnomAD) were selected for further analysis. Prediction of variant deleteriousness was assessed by 4 algorithms (Provean, SIFT, Polyphen-2, CADD). Results: Filtering of 32,788 non-synonymous, likely germline variants produced 148 that occurred at a higher frequency in our cohort than in the general population (p < 0.01, Fisher's exact test). Of these, 29 were predicted to be pathogenic in 3 out of 4 algorithms. Five unrelated individuals were found to harbor a heterozygous p.Leu2307Phe variant in the ATM gene (chr11:108326169 C>T). The clinical characteristics of these individuals are presented in Table 1. The structure prediction of ATM indicates that Ser2306 is a potential phosphorylation site of protein kinase A, suggesting that the methionine-aromatic bond between M2026 and the mutated F2307 may block the phosphorylation of S2306 (Figure 1). Conclusions: We identified a rare ATM germline variant (chr11:108326169 C>T; p.Leu2307Phe) present in 5 individuals with familial MPN. ATM is involved in DNA damage repair and important in the maintenance of genomic integrity. Heterozygous germline variants in ATM are known to predispose to multiple cancer types, including breast, prostate, pancreatic and melanoma. Further, common polymorphisms in ATM have been found to be associated with the MPN phenotype via GWAS. Our data suggests that this variant may impact ATM activation and its function in DNA damage repair, and functional studies are in progress. These data implicate a rare germline ATM variant as a novel risk factor for development of MPN. Figure 1 Figure 1. Disclosures Hourigan: Sellas: Research Funding.

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A novel germline mutation in the POT1 gene predisposes to familial non-medullary thyroid cancer

10.1101/2020.03.23.004663 ◽

2020 ◽

Author(s):

Aayushi Srivastava ◽

Beiping Miao ◽

Diamanto Skopelitou ◽

Varun Kumar ◽

Abhishek Kumar ◽

...

Keyword(s):

Thyroid Cancer ◽

Genetic Basis ◽

Medullary Thyroid Cancer ◽

Whole Genome ◽

Telomere Dysfunction ◽

Wild Type ◽

Medullary Thyroid ◽

Wild Type Counterpart ◽

Protection Of Telomeres 1

AbstractNon-medullary thyroid cancer (NMTC) is a common endocrine malignancy with a genetic basis that has yet to be unequivocally established. In a recent whole genome sequencing study of five families with recurrence of NMTCs, we shortlisted promising variants with the help of bioinformatics tools. Here, we report in silico analyses and in vitro experiments on a novel germline variant (p.V29L) in the highly conserved oligonucleotide/oligosaccharide binding domain of the Protection of Telomeres 1 (POT1) gene in one of the families. The results showed that the variant demonstrates a reduction in telomere-bound POT1 levels in the mutant protein as compared to its wild-type counterpart. HEK293Tcells carrying POT1V29L showed increased telomere length in comparison to wild type cells, strongly suggesting that the mutation causes telomere dysfunction and may play a role in predisposition to NMTC in this family. This study reports the first germline POT1 mutation in a family with a predominance of thyroid cancer, thereby expanding the spectrum of cancers associated with mutations in the shelterin complex.

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