Whole-genome Sequencing of an Aggressive BRAF Wild-type Papillary Thyroid Cancer Identified EML4–ALK Translocation as a Therapeutic Target

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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Overexpression of microRNA‑203 can downregulate survivin and function as a potential therapeutic target in papillary thyroid cancer

Oncology Letters ◽

10.3892/ol.2019.11082 ◽

2019 ◽

Cited By ~ 1

Author(s):

Xianjiang Wu ◽

Lei Dai ◽

Zhoujing Zhang ◽

Jueru Zheng ◽

Jianpei Zhao

Keyword(s):

Thyroid Cancer ◽

Papillary Thyroid Cancer ◽

Therapeutic Target ◽

Papillary Thyroid ◽

Potential Therapeutic Target ◽

And Function

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WGS and RNA Studies Diagnose Noncoding DMD Variants in Males With High Creatine Kinase

Neurology Genetics ◽

10.1212/nxg.0000000000000554 ◽

2021 ◽

Vol 7 (1) ◽

pp. e554

Author(s):

Leigh B. Waddell ◽

Samantha J. Bryen ◽

Beryl B. Cummings ◽

Adam Bournazos ◽

Frances J. Evesson ◽

...

Keyword(s):

Creatine Kinase ◽

Western Blot ◽

Whole Genome Sequencing ◽

Rna Sequencing ◽

Genome Sequencing ◽

Premature Stop Codon ◽

Clinical Severity ◽

Whole Genome ◽

Wild Type ◽

Quantitative Western Blot

ObjectiveTo describe the diagnostic utility of whole-genome sequencing and RNA studies in boys with suspected dystrophinopathy, for whom multiplex ligation-dependent probe amplification and exomic parallel sequencing failed to yield a genetic diagnosis, and to use remnant normal DMD splicing in 3 families to define critical levels of wild-type dystrophin bridging clinical spectrums of Duchenne to myalgia.MethodsExome, genome, and/or muscle RNA sequencing was performed for 7 males with elevated creatine kinase. PCR of muscle-derived complementary DNA (cDNA) studied consequences for DMD premessenger RNA (pre-mRNA) splicing. Quantitative Western blot was used to determine levels of dystrophin, relative to control muscle.ResultsSplice-altering intronic single nucleotide variants or structural rearrangements in DMD were identified in all 7 families. Four individuals, with abnormal splicing causing a premature stop codon and nonsense-mediated decay, expressed remnant levels of normally spliced DMD mRNA. Quantitative Western blot enabled correlation of wild-type dystrophin and clinical severity, with 0%–5% dystrophin conferring a Duchenne phenotype, 10% ± 2% a Becker phenotype, and 15% ± 2% dystrophin associated with myalgia without manifesting weakness.ConclusionsWhole-genome sequencing relied heavily on RNA studies to identify DMD splice-altering variants. Short-read RNA sequencing was regularly confounded by the effectiveness of nonsense-mediated mRNA decay and low read depth of the giant DMD mRNA. PCR of muscle cDNA provided a simple, yet informative approach. Highly relevant to genetic therapies for dystrophinopathies, our data align strongly with previous studies of mutant dystrophin in Becker muscular dystrophy, with the collective conclusion that a fractional increase in levels of normal dystrophin between 5% and 20% is clinically significant.

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AcornHRD: A novel tool to identify homologous recombination deficiency events in whole genome sequencing data.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.e15078 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. e15078-e15078

Author(s):

Kai Liu ◽

Xueyu Hao ◽

Mengmeng Zhang ◽

Mingwei Li ◽

Wang Wang ◽

...

Keyword(s):

Breast Cancer ◽

Ovarian Cancer ◽

Homologous Recombination ◽

Whole Genome Sequencing ◽

Cell Line ◽

Cell Lines ◽

Genome Sequencing ◽

Whole Genome ◽

Wild Type ◽

Homologous Recombination Deficiency

e15078 Background: Recently, homologous recombination deficiency (HRD) scores are associated with the efficacy of Poly‐(ADP‐Ribose)‐Polymerase (PARP) inhibition and platinum-based chemotherapy in a variety of cancers. Evaluating HRD level in patients with cancers is becoming far more important and influential, so far, there is no standard method to be used in clinical. In this study, we developed an algorithm to detect HRD from next-generation sequencing (NGS) for finding additional patients may potentially benefit from target therapy. Methods: Forty-eight patients were enrolled, including breast cancer, ovarian cancer, prostatic cancer. Fifteen cell lines with breast cancer and endometrial carcinoma were collected from Cobioer biosciences co., LTD. Forty-eight Formalin-fixed, paraffin embedded (FFPE) samples and 15 cell lines were performed by DNA extracting. We developed an HRD score algorithm, termed as AcornHRD algorithm. HRD score was analyzed by whole-genome sequencing, and GATK mutect2 software was used to detect BRCA1/2mutation by deep sequencing. Results: BRCA1/2 deleterious mutations were observed in 20 patients (41.7%). HRD was explained by deficiencies in 17 patients (85.0%) with BRCA mutation, whereas eight HRD-high tumors were non- BRCA related (28.6%). Among BRCA wild-type patients, the corresponding percentage of HRD positive patients in breast cancer, ovarian cancer and prostate cancer were 36.3%, 37.5% and 11.1%, respectively. Similar results were also verified in the cell line datasets. The findings showed that 100% (3/3) BRCA1/2 deficient cell lines are also HRD-high. Furthermore, HRD scores were highly correlated with standard results in the cell line datasets. Conclusions: We here report the NGS-based HRD scores to distinguish similarly well between BRCA mutant and BRCA wild-type cases in a cohort of Chinese population. AcornHRD scores were highly associated with BRCA1/2 deficiency. AcornHRD algorithm can be a useful tool to detect HRD events in clinical settings.

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Therapeutic Potential of Dickkopf-1 in Wild-Type BRAF Papillary Thyroid Cancer via Regulation of β-Catenin/E-cadherin Signaling

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jc.2013-4467 ◽

2014 ◽

Vol 99 (9) ◽

pp. E1641-E1649 ◽

Cited By ~ 8

Author(s):

Sun Wook Cho ◽

Young A. Kim ◽

Hyun Jin Sun ◽

Hwa Young Ahn ◽

Eun Kyung Lee ◽

...

Keyword(s):

Thyroid Cancer ◽

Papillary Thyroid Cancer ◽

Therapeutic Potential ◽

Papillary Thyroid ◽

Wild Type ◽

Dickkopf 1 ◽

E Cadherin

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Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers

Nature Biotechnology ◽

10.1038/nbt.2515 ◽

2013 ◽

Vol 31 (4) ◽

pp. 325-330 ◽

Cited By ~ 91

Author(s):

Karl J V Nordström ◽

Maria C Albani ◽

Geo Velikkakam James ◽

Caroline Gutjahr ◽

Benjamin Hartwig ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Wild Type ◽

Sequencing Data ◽

Mutation Identification

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Monitoring Antifungal Resistance in a Global Collection of Invasive Yeasts and Molds: Application of CLSI Epidemiological Cutoff Values and Whole-Genome Sequencing Analysis for Detection of Azole Resistance in Candida albicans

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00906-17 ◽

2017 ◽

Vol 61 (10) ◽

Cited By ~ 34

Author(s):

Mariana Castanheira ◽

Lalitagauri M. Deshpande ◽

Andrew P. Davis ◽

Paul R. Rhomberg ◽

Michael A. Pfaller

Keyword(s):

Candida Albicans ◽

Whole Genome Sequencing ◽

Amphotericin B ◽

Genome Sequencing ◽

Azole Resistance ◽

Whole Genome ◽

Sequencing Analysis ◽

Wild Type ◽

Content Type ◽

Yeasts And Molds

ABSTRACT The activity of 7 antifungal agents against 3,557 invasive yeasts and molds collected in 29 countries worldwide in 2014 and 2015 was evaluated. Epidemiological cutoff values (ECVs) published in the Clinical and Laboratory Standards Institute (CLSI) M59 document were applied for species with no clinical breakpoints. Echinocandin susceptibility rates were 95.9% to 100.0% for the 5 most common Candida species, except for the rates for Candida parapsilosis to anidulafungin (88.7% susceptible, 100.0% wild type). Rates of fluconazole resistance ranged from 8.0% for Candida glabrata to 0.4% for Candida albicans. Seven Candida species displayed 100.0% wild-type amphotericin B MIC results, and Candida dubliniensis and Candida lusitaniae exhibited wild-type echinocandin MIC results. The highest fluconazole, voriconazole, and posaconazole MIC values for Cryptococcus neoformans var. grubii were 8 μg/ml, 0.12 μg/ml, and 0.25 μg/ml, respectively. Aspergillus fumigatus isolates were 100.0% wild type for caspofungin and amphotericin B, but 3 (0.8%) of these isolates were non-wild type to itraconazole (2 isolates) or voriconazole (1 isolate). Mutations in FKS hot spot (HS) regions were detected among 13/20 Candida isolates displaying echinocandin MICs greater than the ECV (16 of these 20 isolates were C. glabrata). Most isolates carrying mutations in FKS HS regions were resistant to 2 or more echinocandins. Five fluconazole-nonsusceptible C. albicans isolates were submitted to whole-genome sequencing analysis. Gain-of-function, Erg11 heterozygous, and Erg3 homozygous mutations were observed in 1 isolate each. One isolate displayed MDR1 promoter allele alterations associated with azole resistance. Elevated levels of expression of MDR1 or CDR2 were observed in 3 isolates and 1 isolate, respectively. Echinocandin and azole resistance is still uncommon among contemporary fungal isolates; however, mechanisms of resistance to antifungals were observed among Candida spp., showing that resistance can emerge and monitoring is warranted.

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BRAF V600E and Retinoic Acid in Radioiodine-Refractory Papillary Thyroid Cancer

Hormone and Metabolic Research ◽

10.1055/a-0765-9078 ◽

2018 ◽

Vol 51 (01) ◽

pp. 69-75 ◽

Cited By ~ 2

Author(s):

Jan Groener ◽

Debora Gelen ◽

Carolin Mogler ◽

Esther Herpel ◽

Csaba Toth ◽

...

Keyword(s):

Thyroid Cancer ◽

Retinoic Acid ◽

Papillary Thyroid Cancer ◽

Initial Response ◽

University Hospital ◽

Braf V600e ◽

Papillary Thyroid ◽

Wild Type ◽

Mutational Status ◽

Before And After

AbstractRadioiodine refractoriness in differentiated thyroid cancer remains an unsolved therapeutic problem. Response to retinoids might depend on specific genetic markers. In this retrospective analysis, associations between BRAF V600E and clinical outcomes after redifferentiation with retinoic acid (RA) and radioiodine therapy (RIT) were investigated. Thirteen patients with radioiodine-refractory (RAI-R) papillary thyroid cancer (PTC) were treated with 13-cis-RA followed by iodine-131 treatment at the Department of Endocrinology, Heidelberg University Hospital, Heidelberg, Germany. DNA sequencing was performed in formalin-fixed paraffin-embedded tissue. Clinical outcome parameters were tumor size, thyroglobulin, and radioiodine uptake in correlation to mutational status. Differences of each parameter were compared before and after RA/RIT. Initial response showed no difference in patients with BRAF V600E compared to patients with wild type. However, after a median follow-up of 2 and a half years, 2 out of 3 patients with BRAF V600E showed response compared to 5 out of 9 with wild type under consideration of all 3 parameters. In this small cohort, more RAI-R PTC patients with BRAF V600E receiving redifferentiation therapy showed response. Verification in a larger study population analyzing mutational status in patients with RAI-R PTC might be helpful to identify patients where redifferentiation therapy might lead to an improved outcome.

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Burkholderia pseudomallei Isolates from Sarawak, Malaysian Borneo, Are Predominantly Susceptible to Aminoglycosides and Macrolides

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01842-13 ◽

2013 ◽

Vol 58 (1) ◽

pp. 162-166 ◽

Cited By ~ 32

Author(s):

Yuwana Podin ◽

Derek S. Sarovich ◽

Erin P. Price ◽

Mirjam Kaestli ◽

Mark Mayo ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Burkholderia Pseudomallei ◽

Sequence Type ◽

Clinical Isolates ◽

Whole Genome ◽

Wild Type ◽

Content Type ◽

District Hospitals ◽

Malaysian Borneo

ABSTRACTMelioidosis is a potentially fatal disease caused by the saprophytic bacteriumBurkholderia pseudomallei. Resistance to gentamicin is generally a hallmark ofB. pseudomallei, and gentamicin is a selective agent in media used for diagnosis of melioidosis. In this study, we determined the prevalence and mechanism of gentamicin susceptibility found inB. pseudomalleiisolates from Sarawak, Malaysian Borneo. We performed multilocus sequence typing and antibiotic susceptibility testing on 44B. pseudomalleiclinical isolates from melioidosis patients in Sarawak district hospitals. Whole-genome sequencing was used to identify the mechanism of gentamicin susceptibility. A novel allelic-specific PCR was designed to differentiate gentamicin-sensitive isolates from wild-typeB. pseudomallei. A reversion assay was performed to confirm the involvement of this mechanism in gentamicin susceptibility. A substantial proportion (86%) ofB. pseudomalleiclinical isolates in Sarawak, Malaysian Borneo, were found to be susceptible to the aminoglycoside gentamicin, a rare occurrence in other regions whereB. pseudomalleiis endemic. Gentamicin sensitivity was restricted to genetically related strains belonging to sequence type 881 or its single-locus variant, sequence type 997. Whole-genome sequencing identified a novel nonsynonymous mutation withinamrB, encoding an essential component of the AmrAB-OprA multidrug efflux pump. We confirmed the role of this mutation in conferring aminoglycoside and macrolide sensitivity by reversion of this mutation to the wild-type sequence. Our study demonstrates that alternativeB. pseudomalleiselective media without gentamicin are needed for accurate melioidosis laboratory diagnosis in Sarawak. This finding may also have implications for environmental sampling of other locations to test forB. pseudomalleiendemicity.

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