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Article: Modifier genes and Lynch syndrome: some considerations.

Scott, Rodney J

2022 Volume 20, Issue 1, Page(s) 35

Abstract: Lynch Syndrome (LS) is a highly variable entity with some patients presenting at very young ages with malignancy whereas others may never develop a malignancy yet carry an unequivocal genetic predisposition to disease. The most frequent LS malignancy ... ...

Abstract	Lynch Syndrome (LS) is a highly variable entity with some patients presenting at very young ages with malignancy whereas others may never develop a malignancy yet carry an unequivocal genetic predisposition to disease. The most frequent LS malignancy remains colorectal cancer, a disease that is thought to involve genetic as well as environmental factors in its aetiology. Environmental insults are undeniably associated with cancer risk, especially those imparted by such activities as smoking and excessive alcohol consumption. Notwithstanding, in an inherited predisposition the expected exposures to an environmental insult are considered to be complex and require knowledge about the respective exposure and how it might interact with a genetic predisposition. Typically, smoking is one of the major confounders when considering environmental factors that can influence disease expression on a background of significant genetic risk. In addition to environmental triggers, the risk of developing a malignancy for people carrying an inherited predisposition to disease can be influenced by additional genetic factors that do not necessarily segregate with a disease predisposition allele. The purpose of this review is to examine the current state of modifier gene detection in people with a genetic predisposition to develop LS and present some data that supports the notion that modifier genes are gene specific thus explaining why some modifier gene studies have failed to identify associations when this is not taken into account.
Language	English
Publishing date	2022-09-10
Publishing country	Poland
Document type	Journal Article ; Review
ZDB-ID	2252512-9
ISSN	1897-4287 ; 1731-2302
ISSN (online)	1897-4287
ISSN	1731-2302
DOI	10.1186/s13053-022-00240-2
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Article ; Online: Reply to "Implementation of DPYD Genotyping in Admixed American Populations: Brazil as a Model Case".

White, Cassandra / Scott, Rodney J / Paul, Christine / Ackland, Stephen

Clinical pharmacology and therapeutics

2023 Volume 114, Issue 1, Page(s) 25

MeSH term(s)	Humans ; Genotype ; Brazil ; Capecitabine ; Fluorouracil
Chemical Substances	Capecitabine (6804DJ8Z9U) ; Fluorouracil (U3P01618RT)
Language	English
Publishing date	2023-05-10
Publishing country	United States
Document type	Letter
ZDB-ID	123793-7
ISSN	1532-6535 ; 0009-9236
ISSN (online)	1532-6535
ISSN	0009-9236
DOI	10.1002/cpt.2922
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Zs.A 20: Show issues

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Article ; Online: The utilisation of digital droplet PCR to enhance the diagnosis of bladder and pancreaticobiliary tumours in cytology specimens.

Weigner, Julie / Billings, Raewyn / Scott, Rodney J / King, Simon

Diagnostic cytopathology

2023 Volume 51, Issue 8, Page(s) 511–518

Abstract: Background: Digital droplet PCR (ddPCR) is a relatively new technique used to detect molecular alterations with unprecedented precision and accuracy. It is particularly useful for detecting point mutations and copy number variation (CNV) in samples with ...

Abstract	Background: Digital droplet PCR (ddPCR) is a relatively new technique used to detect molecular alterations with unprecedented precision and accuracy. It is particularly useful for detecting point mutations and copy number variation (CNV) in samples with small amounts of target DNA. This proof of principle study was conducted to see if ddPCR technology could be applied to cytology specimens to detect molecular alterations which may influence diagnostic decision making. Methods: A range of cytological specimens derived from bladder or pancreaticobiliary origin, with varying diagnoses but with an emphasis on abnormality, underwent ddPCR testing. DNA was manually extracted from Thinprep vials, cell blocks or direct fine needle aspiration smears. ddPCR was performed using two somatic point mutations TP53 R248W and TP53 R273H assays for both urine and pancreaticobiliary cytology specimens. Three CNV assays; CDKN2A, E2F3 and YWHAZ were applied to urine samples. SMAD4 and CDKN2A CNVs were applied to the pancreaticobiliary samples. Results: 16 of 21 urine specimens showed molecular alterations using ddPCR testing. 12 of those 16 cases were associated with malignant outcomes. The pancreaticobiliary specimens showed 14 of 37 specimens with molecular alterations, all of which were associated with carcinoma. We demonstrated an increasing percentage of molecular aberrations associated with increasing severity of cytological results. Conclusion: Our results have shown that ddPCR can identify both mutations and CNVs in urine and pancreaticobiliary cytology derived samples. Being able to detect these molecular alterations may reduce the number of equivocal results leading to more timely and informed patient management decisions.
MeSH term(s)	Humans ; Urinary Bladder ; DNA Copy Number Variations/genetics ; Polymerase Chain Reaction/methods ; Mutation ; Carcinoma
Language	English
Publishing date	2023-05-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	632710-2
ISSN	1097-0339 ; 8755-1039
ISSN (online)	1097-0339
ISSN	8755-1039
DOI	10.1002/dc.25151
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Zs.A 2117: Show issues

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Article ; Online: Exome sequencing of familial adenomatous polyposis-like individuals identifies both known and novel causative genes.

Xavier, Alexandre / Scott, Rodney J / Talseth-Palmer, Bente

Clinical genetics

2021 Volume 100, Issue 4, Page(s) 478–483

Abstract: Inherited polyposis syndromes are predominantly caused by pathogenic variants in APC and are linked to familial adenomatous polyposis (FAP). However, after clinical screening, 20%-30% of individuals diagnosed with FAP do not carry a pathogenic variant in ...

Abstract	Inherited polyposis syndromes are predominantly caused by pathogenic variants in APC and are linked to familial adenomatous polyposis (FAP). However, after clinical screening, 20%-30% of individuals diagnosed with FAP do not carry a pathogenic variant in APC (often categorised as FAP-like). Other known inherited adenomatous polyposis syndromes such as MUTYH, POLD1/E, or NTHL1-associated polyposis only account for, 3 a fraction of the remaining cases. A cohort of 48 individuals clinically diagnosed with a FAP-like phenotype was selected based on a strong family history of colorectal cancer and no previous pathogenic variant found in APC and/or MUTYH, by genetic screening. Using whole exome sequencing, FAP-like patients were found to carry pathogenic variants in MUTYH, APC, POLE and TP53, as well as DNA-repair genes and inflammation related genes. Additionally, a comprehensive assessment of copy number variation revealed two loci of interest that appeared to be associated with polyposis risk. In total, 6 out of 48 polyposis were explained through re-sequencing. This study highlights the potential role of DNA-repair as well as inflammation-related variants towards polyp development.
MeSH term(s)	Adenomatous Polyposis Coli/diagnosis ; Adenomatous Polyposis Coli/genetics ; Alleles ; Amino Acid Substitution ; DNA Copy Number Variations ; DNA Glycosylases/genetics ; Genes, APC ; Genetic Association Studies ; Genetic Predisposition to Disease ; Humans ; Mutation ; Phenotype ; Sequence Analysis, DNA ; Whole Exome Sequencing
Chemical Substances	DNA Glycosylases (EC 3.2.2.-) ; mutY adenine glycosylase (EC 3.2.2.-)
Language	English
Publishing date	2021-07-26
Publishing country	Denmark
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	221209-2
ISSN	1399-0004 ; 0009-9163
ISSN (online)	1399-0004
ISSN	0009-9163
DOI	10.1111/cge.14029
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Article ; Online: Detection of germline variants with pathogenic potential in 48 patients with familial colorectal cancer by using whole exome sequencing.

Singh, Ashish Kumar / Talseth-Palmer, Bente / Xavier, Alexandre / Scott, Rodney J / Drabløs, Finn / Sjursen, Wenche

BMC medical genomics

2023 Volume 16, Issue 1, Page(s) 126

Abstract: Background: Hereditary genetic mutations causing predisposition to colorectal cancer are accountable for approximately 30% of all colorectal cancer cases. However, only a small fraction of these are high penetrant mutations occurring in DNA mismatch ... ...

Abstract	Background: Hereditary genetic mutations causing predisposition to colorectal cancer are accountable for approximately 30% of all colorectal cancer cases. However, only a small fraction of these are high penetrant mutations occurring in DNA mismatch repair genes, causing one of several types of familial colorectal cancer (CRC) syndromes. Most of the mutations are low-penetrant variants, contributing to an increased risk of familial colorectal cancer, and they are often found in additional genes and pathways not previously associated with CRC. The aim of this study was to identify such variants, both high-penetrant and low-penetrant ones. Methods: We performed whole exome sequencing on constitutional DNA extracted from blood of 48 patients suspected of familial colorectal cancer and used multiple in silico prediction tools and available literature-based evidence to detect and investigate genetic variants. Results: We identified several causative and some potentially causative germline variants in genes known for their association with colorectal cancer. In addition, we identified several variants in genes not typically included in relevant gene panels for colorectal cancer, including CFTR, PABPC1 and TYRO3, which may be associated with an increased risk for cancer. Conclusions: Identification of variants in additional genes that potentially can be associated with familial colorectal cancer indicates a larger genetic spectrum of this disease, not limited only to mismatch repair genes. Usage of multiple in silico tools based on different methods and combined through a consensus approach increases the sensitivity of predictions and narrows down a large list of variants to the ones that are most likely to be significant.
MeSH term(s)	Humans ; Colorectal Neoplasms, Hereditary Nonpolyposis/diagnosis ; Colorectal Neoplasms, Hereditary Nonpolyposis/genetics ; Exome Sequencing ; Genetic Predisposition to Disease ; Pedigree ; Germ-Line Mutation ; Germ Cells ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/diagnosis
Language	English
Publishing date	2023-06-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2411865-5
ISSN	1755-8794 ; 1755-8794
ISSN (online)	1755-8794
ISSN	1755-8794
DOI	10.1186/s12920-023-01562-3
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Article ; Online: Evaluation of a Multi-Gene Methylation Blood-Test for the Detection of Colorectal Cancer.

Petit, Joel / Carroll, Georgia / Williams, Henry / Pockney, Peter / Scott, Rodney J

Medical sciences (Basel, Switzerland)

2023 Volume 11, Issue 3

Abstract: Circulating tumour DNA biomarkers are an expanding field in oncology research that offer great potential but are currently often limited in value by overall cost. The aim of this study was to evaluate the efficacy of a novel multi-gene methylation blood ... ...

Abstract	Circulating tumour DNA biomarkers are an expanding field in oncology research that offer great potential but are currently often limited in value by overall cost. The aim of this study was to evaluate the efficacy of a novel multi-gene methylation blood test for the identification of colorectal cancer and throughout the spectrum of colorectal disease. Participants were recruited either prior to resection for known CRC or prior to screening colonoscopy after a positive faecal immunochemical test. Blood was collected from participants prior to their procedure being performed. The plasma was separated, and multiplex MethylLight droplet digital PCR was used to analyse for the presence of four methylated genes:
MeSH term(s)	Humans ; Methylation ; Hematologic Tests ; Circulating Tumor DNA/genetics ; Colonic Diseases ; Cytoskeletal Proteins ; Colorectal Neoplasms/diagnosis ; Colorectal Neoplasms/genetics
Chemical Substances	Circulating Tumor DNA ; Cytoskeletal Proteins
Language	English
Publishing date	2023-09-15
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2754473-4
ISSN	2076-3271 ; 2076-3271
ISSN (online)	2076-3271
ISSN	2076-3271
DOI	10.3390/medsci11030060
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Article: Verification and Validation of a Four-Gene Panel as a Prognostic Indicator in Triple Negative Breast Cancer.

Pariyar, Mamta / Thorne, Rick F / Scott, Rodney J / Avery-Kiejda, Kelly A

Frontiers in oncology

2022 Volume 12, Page(s) 821334

Abstract: Triple negative breast cancer (TNBC) is a highly aggressive subtype with a high rate of metastasis, early distant recurrence and resistance to therapy leading to worse survival than other breast cancer subtypes. There are no well-established biomarkers ... ...

Abstract	Triple negative breast cancer (TNBC) is a highly aggressive subtype with a high rate of metastasis, early distant recurrence and resistance to therapy leading to worse survival than other breast cancer subtypes. There are no well-established biomarkers that can determine women who will do better and those who are likely to have poorer outcomes with TNBC, nor are there targeted therapies. Thus, the identification of prognostic and/or predictive biomarkers will enable tailored therapies based on their likelihood of disease outcomes and may prevent over- and under-diagnosis. Previous studies from our laboratory have identified four genes (ANP32E, DSC2, ANKRD30A and IL6ST/gp130) that are specific to TNBC and were associated with lymph node metastasis (LNmets), the earliest indicator of tumor progression
Language	English
Publishing date	2022-03-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2022.821334
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Article ; Online: Prevalence and clinical significance of co-existing mutations in

Jamaluddin, M Fairuz B / Nagendra, Prathima B / Ko, Yi-An / Bajwa, Preety / Scott, Rodney J / Nahar, Pravin / Tanwar, Pradeep S

Frontiers in reproductive health

2023 Volume 5, Page(s) 1081092

Abstract: Uterine fibroids are exceedingly common benign tumours of the female reproductive system and cause severe symptoms, including acute pain, bleeding, and infertility. Fibroids are frequently associated with genetic alterations affecting mediator complex ... ...

Abstract	Uterine fibroids are exceedingly common benign tumours of the female reproductive system and cause severe symptoms, including acute pain, bleeding, and infertility. Fibroids are frequently associated with genetic alterations affecting mediator complex subunit 12 (
Language	English
Publishing date	2023-04-11
Publishing country	Switzerland
Document type	Journal Article
ISSN	2673-3153
ISSN (online)	2673-3153
DOI	10.3389/frph.2023.1081092
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Article ; Online: Overview of genetic markers for hereditary colorectal cancer

Scott Rodney J

Hereditary Cancer in Clinical Practice , Vol 10, Iss Suppl 4, p A

2012 Volume 22

Keywords	Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282 ; Internal medicine ; RC31-1245 ; Medicine ; R ; DOAJ:Oncology ; DOAJ:Medicine (General) ; DOAJ:Health Sciences
Language	English
Publishing date	2012-12-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: TAPES: A tool for assessment and prioritisation in exome studies.

Xavier, Alexandre / Scott, Rodney J / Talseth-Palmer, Bente A

PLoS computational biology

2019 Volume 15, Issue 10, Page(s) e1007453

Abstract: Next-generation sequencing continues to grow in importance for researchers. Exome sequencing became a widespread tool to further study the genomic basis of Mendelian diseases. In an effort to identify pathogenic variants, reject benign variants and ... ...

Abstract	Next-generation sequencing continues to grow in importance for researchers. Exome sequencing became a widespread tool to further study the genomic basis of Mendelian diseases. In an effort to identify pathogenic variants, reject benign variants and better predict variant effects in downstream analysis, the American College of Medical Genetics (ACMG) published a set of criteria in 2015. While there are multiple publicly available software's available to assign the ACMG criteria, most of them do not take into account multi-sample variant calling formats. Here we present a tool for assessment and prioritisation in exome studies (TAPES, https://github.com/a-xavier/tapes), an open-source tool designed for small-scale exome studies. TAPES can quickly assign ACMG criteria using ANNOVAR or VEP annotated files and implements a model to transform the categorical ACMG criteria into a continuous probability, allowing for a more accurate classification of pathogenicity or benignity of variants. In addition, TAPES can work with cohorts sharing a common phenotype by utilising a simple enrichment analysis, requiring no controls as an input as well as providing powerful filtering and reporting options. Finally, benchmarks showed that TAPES outperforms available tools to detect both pathogenic and benign variants, while also integrating the identification of enriched variants in study cohorts compared to the general population, making it an ideal tool to evaluate a smaller cohort before using bigger scale studies.
MeSH term(s)	Computational Biology/methods ; Exome/genetics ; Genetic Variation/genetics ; Genome, Human/genetics ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods ; Software
Language	English
Publishing date	2019-10-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1007453
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