Constitutional chromothripsis of the APC locus as a cause of genetic predisposition to colon cancer

PurposeApproximately 20% of patients with clinical familial adenomatous polyposis (FAP) remain unsolved after molecular genetic analysis of the APC and other polyposis genes, suggesting additional pathomechanisms.MethodsWe applied multidimensional genomic analysis employing chromosomal microarray profiling, optical mapping, long-read genome and RNA sequencing combined with FISH and standard PCR of genomic and complementary DNA to decode a patient with an attenuated FAP that had remained unsolved by Sanger sequencing and multigene panel next-generation sequencing for years.ResultsWe identified a complex 3.9 Mb rearrangement involving 14 fragments from chromosome 5q22.1q22.3 of which three were lost, 1 reinserted into chromosome 5 and 10 inserted into chromosome 10q21.3 in a seemingly random order and orientation thus fulfilling the major criteria of chromothripsis. The rearrangement separates APC promoter 1B from the coding ORF (open reading frame) thus leading to allele-specific downregulation of APC mRNA. The rearrangement also involves three additional genes implicated in the APC–Axin–GSK3B–β-catenin signalling pathway.ConclusionsBased on comprehensive genomic analysis, we propose that constitutional chromothripsis dampening APC expression, possibly modified by additional APC–Axin–GSK3B–β-catenin pathway disruptions, underlies the patient’s clinical phenotype. The combinatorial approach we deployed provides a powerful tool set for deciphering unsolved familial polyposis and potentially other tumour syndromes and monogenic diseases.

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Gene mutations in the PI3K/Akt signaling pathway were related to immune thrombocytopenia pathogenesis

10.21203/rs.3.rs-131436/v1 ◽

2020 ◽

Author(s):

Ruijie Sun ◽

Shu-Yan Liu ◽

Xiao-Mei Zhang ◽

Jing-Jing Zhu ◽

Dai Yuan ◽

...

Keyword(s):

Genetic Susceptibility ◽

Signaling Pathway ◽

Molecular Genetic ◽

Genomic Analysis ◽

Akt Signaling ◽

Molecular Genetic Analysis ◽

Missense Mutations ◽

Functional Connections ◽

Molecular Features ◽

The Impact

Abstract Immune thrombocytopenic (ITP) is an autoimmune bleeding disease with genetic susceptibility. In this research, we conducted an in-depth genomic analysis of a cohort of patients and elucidate molecular features associated with disease pathogenesis of ITP. High-molecular-weight genomic DNA was extracted from freshly frozen BMBMCs (bone marrow blood mononuclear cell) in 20 active ITP patients. After this, the samples were subjected to molecular genetic analysis by whole-exome sequencing technique (WES) then, confirmed by sanger sequencing method. The enriched signaling pathway analysis and cellular processes associated with the mutated genes was performed with gene mapping to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The results of this study showed that there were 3998 missense mutations involving 2269 genes in more than 10 individuals. Unique genetic variants including PTEN, INSR and COCH were the most associated with the pathogenesis of ITP. Functional analysis revealed these mutation genes mainly affect Phosphatidylinositol 3 kinase/serine/threonine kinase B (PI3K/Akt) signaling pathways (signal transduction) and platelet activation (immune system). Our finding further demonstrates the functional connections between these variant genes and ITP. Although the substantial mechanism and the impact of genetic variation are required further investigation, the application of next generation sequencing in ITP in this paper is a valuable method to reveal the genetic susceptibility.

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Variant Phasing and Haplotypic Expression from Single-molecule Long-read Sequencing in Maize

10.1101/654533 ◽

2019 ◽

Cited By ~ 2

Author(s):

Bo Wang ◽

Elizabeth Tseng ◽

Primo Baybayan ◽

Kevin Eng ◽

Michael Regulski ◽

...

Keyword(s):

Single Molecule ◽

Genomic Analysis ◽

Full Length ◽

Specific Gene ◽

Population Genetic Analysis ◽

Functional Genomic Analysis ◽

Long Read ◽

Allele Specific ◽

Regulatory Effects ◽

Hybrid Lines

AbstractHaplotype phasing of genetic variants in maize is important for interpretation of the genome, population genetic analysis and functional genomic analysis of allelic activity. Accordingly, accurate methods for phasing the full-length isoforms are essential for functional genomics studies. We performed an isoform-level phasing study in maize, using two inbred lines and their reciprocal crosses, based on the single-molecule full-length cDNA sequencing. To phase and analyze the full-length transcripts between hybrids and parents, we developed a tool called IsoPhase. Using this tool, we validated the majority of SNPs called against matching short-read data and identified cases of allele-specific, gene-level and isoform-level expression. Our results revealed that maize parental lines and hybrid lines exhibit different splicing activities. After phasing 6,907 genes in two reciprocal hybrids using embryo, endosperm and root tissues, we annotated the SNPs and identified large-effect genes. In addition, based on single-molecule sequencing, we identified parent-of-origin isoforms in maize hybrids, distinct novel isoforms in maize parent and hybrid lines, and imprinted genes from different tissues. Finally, we characterized variation in cis- and trans-regulatory effects. Our study provides measures of haplotypic expression that could increase accuracy in studies of allelic expression.

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Molecular Genetic Analysis of Drosophila ash2, a Member of the Trithorax Group Required for Imaginal Disc Pattern Formation

Genetics ◽

10.1093/genetics/144.2.621 ◽

1996 ◽

Vol 144 (2) ◽

pp. 621-633 ◽

Cited By ~ 4

Author(s):

Amy L Adamson ◽

Allen Shearn

Keyword(s):

Pattern Formation ◽

Fat Body ◽

Polyclonal Antibodies ◽

Molecular Genetic ◽

Molecular Genetic Analysis ◽

Polycomb Group ◽

Trithorax Group ◽

Phd Finger ◽

Reading Frame ◽

Active Transcription

Abstract The ash2 gene is a member of the trithorax group of genes whose products function to maintain active transcription of homeotic selector genes. Mutations in ash2 cause the homeotic transformations expected for a gene in this group but, in addition, cause a variety of pattern formation defects that are not necessarily expected. The ash2 gene is located in cytogenetic region 96A17–19 flanked by slowpoke and tolloid and is included in a cosmid that contains part of slowpoke. The ash2 transcript is 2.0 kb and is present throughout development. The ASH2 protein predicted from the nucleotide sequence of the open reading frame has a putative double zinc-finger domain, called a PHD finger, that is present not only in the products of other trithorax group genes such as TRX and MH1, but also in the product of a Polycomb group gene, PCL. Polyclonal antibodies directed against ASH2 detect the protein in imaginal discs and in the nuclei of salivary gland and fat body cells. On immunoblots these affinity-purified antibodies detect a 70-kDa protein in larvae and a 53-kDa protein in pupae.

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proovframe: frameshift-correction for long-read (meta)genomics

10.1101/2021.08.23.457338 ◽

2021 ◽

Author(s):

Thomas Hackl ◽

Florian Trigodet ◽

A Murat Eren ◽

Steven J Biller ◽

John M Eppley ◽

...

Keyword(s):

Gene Prediction ◽

Genomic Analysis ◽

Community Members ◽

Reading Frame ◽

Complex Samples ◽

Small Indels ◽

Sequencing Technologies ◽

Long Reads ◽

Long Read ◽

Improving Accuracy

Long-read sequencing technologies hold big promises for the genomic analysis of complex samples such as microbial communities. Yet, despite improving accuracy, basic gene prediction on long-read data is still often impaired by frameshifts resulting from small indels. Consensus polishing using either complementary short reads or to a lesser extent the long reads themselves can mitigate this effect but requires universally high sequencing depth, which is difficult to achieve in complex samples where the majority of community members are rare. Here we present proovframe, a software implementing an alternative approach to overcome frameshift errors in long-read assemblies and raw long reads. We utilize protein-to-nucleotide alignments against reference databases to pinpoint indels in contigs or reads and correct them by deleting or inserting 1-2 bases, thereby conservatively restoring reading-frame fidelity in aligned regions. Using simulated and real-world benchmark data we show that proovframe performs comparably to short-read-based polishing on assembled data, works well with remote protein homologs, and can even be applied to raw reads directly. Together, our results demonstrate that protein-guided frameshift correction significantly improves the analyzability of long-read data both in combination with and as an alternative to common polishing strategies. Proovframe is available from https://github.com/thackl/proovframe.

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Monogenic diabetes associated with PAX4 gene mutations (MODY9): first description in Russia

Diabetes Mellitus ◽

10.14341/dm9322 ◽

2017 ◽

Vol 20 (5) ◽

pp. 384-387

Author(s):

Natalya A. Zubkova ◽

Olesya A. Gioeva ◽

Vasiliy M. Petrov ◽

Evgeny V. Vasiliev ◽

Alexei V. Timofeev ◽

...

Keyword(s):

Pancreatic Beta Cells ◽

Novel Mutation ◽

Pancreatic Beta Cell ◽

Molecular Genetic ◽

Gene Mutations ◽

Russian Literature ◽

Molecular Genetic Analysis ◽

Dominant Type ◽

Genetic Characteristics ◽

Monogenic Diseases

Maturity-onset diabetes of the young (MODY) is a heterogeneous group of disorders characterised by autosomal dominant type of inheritance and caused by genetic defects leading to dysfunction of pancreatic beta-cells. To date, at least 13 subtypes of MODY have been described in the literature, the most frequent of which are MODY types 13. MODY2 and MODY3 are the most prevalent subtypes, and were previously described in our country, Russia. Several cases of rare MODY subtypes were subsequently described in the Russian literature. The current report is the first in the Russian literature to present clinical and molecular genetic characteristics of two cases of another rare MODY subtypeMODY9. This type of MODY is associated with mutations in the PAX4 gene, which encodes transcription factor PAX4, one of the factors essential for pancreatic beta-cell differentiation. Molecular genetic analysis was performed using next-generation sequencing, a new method recently applied to verify monogenic diseases and, in particular, MODY. This study reports a novel mutation in the PAX4 gene in MODY patients.

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Clinical and molecular genetic characteristics of MODY cases with digenic and oligogenic inheritance as defined by targeted next-generation sequencing

Problems of Endocrinology ◽

10.14341/probl201662620-27 ◽

2017 ◽

Vol 62 (6) ◽

pp. 20-27 ◽

Cited By ~ 1

Author(s):

Olesya A. Gioeva ◽

Natalya A. Zubkova ◽

Yulia V. Tikhonovich ◽

Vasiliy M. Petrov ◽

Evgeniy V. Vasilyev ◽

...

Keyword(s):

Next Generation Sequencing ◽

Genetic Analysis ◽

Candidate Genes ◽

Molecular Genetic ◽

Molecular Genetic Analysis ◽

Simultaneous Analysis ◽

Next Generation ◽

Monogenic Diseases ◽

Oligogenic Inheritance ◽

Generation Sequencing

The diagnosis of MODY should be verified by molecular genetic analysis. Recently the introduction of next-generation sequencing, allowing simultaneous analysis of several candidate genes, greatly facilitates the diagnosis of monogenic diseases including MODY. In addition, the simultaneous analysis of several candidate genes allows to identify cases with digenic and oligogenic inheritance. In this work we present the first description of MODY cases with digenic and oligogenic inheritance in our country.Aim — to characterize MODY cases with digenic and oligogenic inheritance as defined by targeted next-generation sequencing.Material and methods. 256 subjects (age range, 0.3—25 yrs; males, n=149, females, n=107) were included in the study. The patients fulfilled the following MODY criteria: diabetes or intermediate hyperglycemia, absence of β-cell autoimmunity (ICA, GAD, IA2, IAA antibodies), preserved C-peptide secretion. Molecular genetic analysis was performed by next-generation sequencing using custom Ion Ampliseq gene panel and PGM semiconductor sequencer (Ion Torrent). All mutations were confirmed by Sanger sequencing.Results. 10 patients (8 probands, 1 sibling and 1 parent) showed digenic inheritance of MODY: 3 patients with combination of mutations in 2 candidate genes of MODY, 7 — in a candidate genes of MODY and another gene, associated with diabetes mellitus. In 1 case (sibling) showed oligogenic inheritance (mutations in GCK, HNF4A and INSR genes). Seven of the identified mutations were not previously described.Conclusion. Next-generation sequencing is useful in identifying of MODY cases with digenic and oligogenic inheritance, which is extremely important with potentially modifying effect on the phenotype.

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COMPARISON OF DIFFERENT METHODS OF MOLECULAR-GENETIC ANALYSIS OF SOMATIC MUTATIONS IN K-RAS GENE IN PATIENTS WITH COLORECTAL CANCER

Annals of the Russian academy of medical sciences ◽

10.15690/vramn.v67i2.120 ◽

2012 ◽

Vol 67 (2) ◽

pp. 35-41 ◽

Cited By ~ 2

Author(s):

F. A. Amosenko ◽

I. V. Karpov ◽

A. V. Polyakov ◽

S. P. Kovalenko ◽

V. A. Shamanin ◽

...

Keyword(s):

Molecular Genetic ◽

False Negative ◽

Point Mutations ◽

Real Life ◽

Molecular Genetic Analysis ◽

Ras Gene ◽

Specific Pcr ◽

Specificity And Sensitivity ◽

Allele Specific ◽

Allele Specific Pcr

Two approaches to somatic point mutations in 12 and 13 codones of K-ras gene were analyzed: PCR/SSCP/AСRS/sequencing and allele-specific PCR in the real-life regimen (Russian set «KRAS-7M»). The comparison was carried out on 62 examples of genomic DNA extracted from frozen colon carcinomas, which underwent manual dissection. The results obtained in two attempts were consistent in 95,2% (N=59). Specificity and sensitivity of K-ras mutations detection using «KRAS-7M» set were 100 and 96,4% respectively, and 94,1 and 100% respectievly using PCR/SSCP/AСRS/ automatic sequencing. False positive results were absent when detecting with «KRAS-7M» and accounted for 2 cases (5,9%) when using PCR/SSCP/ AСRS/automatic sequencing. The only false negative response (3,6%) was obtained analyzing mutations using «KRAS-7M».

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Molecular Characterization and Genetic Diversity Study in F3 Population of Rice

Progressive Agriculture ◽

10.3329/pa.v20i1-2.16839 ◽

2013 ◽

Vol 20 (1-2) ◽

pp. 1-8

Author(s):

MM Rahman ◽

L Rahman ◽

SN Begum ◽

F Nur

Keyword(s):

Genetic Distance ◽

Gene Diversity ◽

Random Amplified Polymorphic Dna ◽

Molecular Genetic ◽

Molecular Genetic Analysis ◽

Polymorphic Loci ◽

Rice Genotypes ◽

High Level ◽

Genetic Diversity Study ◽

Diversity Study

Random Amplified Polymorphic DNA (RAPD) assay was initiated for molecular genetic analysis among 13 F3 rice lines and their parents. Four out of 15 decamer random primers were used to amplify genomic DNA and the primers yielded a total of 41 RAPD markers of which 37 were considered as polymorphic with a mean of 9.25 bands per primer. The percentage of polymorphic loci was 90.24. The highest percentage of polymorphic loci (14.63) and gene diversity (0.0714) was observed in 05-6 F3 line and the lowest polymorphic loci (0.00) and gene diversity (0.00) was found in 05-12 and 05-15 F3 lines. So, relatively high level of genetic variation was found in 05-6 F3 line and it was genetically more diverse compared to others. The average co-efficient of gene differentiation (GST) and gene flow (Nm) values across all the loci were 0.8689 and 0.0755, respectively. The UPGMA dendrogram based on the Neis genetic distance differentiated the rice genotypes into two main clusters: PNR-519, 05-19, 05-14, 05-12 and 05-17 grouped in cluster 1. On the other hand, Baradhan, 05-9, 05-13, 05-11, 05-5, 05-6, 05-1, 05-4, 05-15 and 05-25 were grouped in cluster 2. The highest genetic distance (0.586) was found between 05-4 and 05-17 F3 lines and they remain in different cluster.DOI: http://dx.doi.org/10.3329/pa.v20i1-2.16839 Progress. Agric. 20(1 & 2): 1 8, 2009

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Diagnosis and Management of Cardiomyopathies – A Focus on Genetics, Cardiac Magnetic Resonance and Clinical Features

European Cardiology Review ◽

10.15420/ecr.2011.7.3.225 ◽

2011 ◽

Vol 7 (3) ◽

pp. 225

Author(s):

Gianfranco Sinagra ◽

Michele Moretti ◽

Giancarlo Vitrella ◽

Marco Merlo ◽

Rossana Bussani ◽

...

Keyword(s):

Clinical Practice ◽

Cardiac Magnetic Resonance ◽

Magnetic Resonance ◽

Imaging Techniques ◽

Molecular Genetic ◽

Molecular Genetic Analysis ◽

Routine Clinical Practice ◽

Clinical Approach ◽

Diagnosis And Management ◽

Made In

In recent years, outstanding progress has been made in the diagnosis and treatment of cardiomyopathies. Genetics is emerging as a primary point in the diagnosis and management of these diseases. However, molecular genetic analyses are not yet included in routine clinical practice, mainly because of their elevated costs and execution time. A patient-based and patient-oriented clinical approach, coupled with new imaging techniques such as cardiac magnetic resonance, can be of great help in selecting patients for molecular genetic analysis and is crucial for a better characterisation of these diseases. This article will specifically address clinical, magnetic resonance and genetic aspects of the diagnosis and management of cardiomyopathies.

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