scholarly journals Rapid and easy detection of the five most common mutations in BRCA1 and BRCA2 genes in the Polish population using CAPS and ACRS-PCR methods

2019 ◽  
Author(s):  
Adam Dąbrowski ◽  
Stanisław Ułaszewski ◽  
Katarzyna Niedźwiecka
Keyword(s):  
Restriction Site ◽  
Restriction Enzymes ◽  
Fast Method ◽  
Brca1 And Brca2 ◽  
Brca1 And Brca2 Genes ◽  
Cleaved Amplified Polymorphic Sequences ◽  
Pcr Techniques ◽  
Created Restriction Site ◽  
Selection Of ◽  
Sequencing Process

In this publication we present a fast method of diagnosing the most common polymorphisms of BRCA1 and BRCA2 genes in Poland – C61G [c.300T>G], C64R [c.190T>C], 4153delA [c.4035delA], 3819del5 [c.3700_3704delGTAAA], and C5972T [c.5744C>T]. Our procedure is based on the use of the cleaved amplified polymorphic sequences (CAPS) and artificially created restriction site (ACRS) PCR techniques. The precise selection of appropriate primer sequences and restriction enzymes enabled specific cuts of DNA fragments. The final quantity and size of the obtained products depend on the presence or the absence of the mutations. The obtained results are unambiguous and do not have to be confirmed by sequencing. The methods of detection of the C61G, C64R, 4153delA, 3819del5, and C5972T mutations in the BRCA1 and BRCA2 genes described by us do not require a sequencing process, which is more expensive, time-consuming and associated with numerous errors. The technique developed by us enables the use of simple electrophoresis for accurate detection of the presence or absence of a specific mutation. Our procedures are fast, precise and unambiguous.

scholarly journals Restriction site-associated DNA from Python-implemented Digestion Simulations (RApyDS): a companion tool for RAD sequencing experimental design

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 360
Author(s):  
Kristianne Arielle Gabriel ◽  
Maria Rejane Nepacina ◽  
Francis Tablizo ◽  
Carlo Lapid ◽  
Mark Lenczner Mendoza ◽  
...  
Keyword(s):  
Restriction Site ◽  
Reference Genome ◽  
Population Genomics ◽  
Restriction Enzymes ◽  
Evaluation Metrics ◽  
Genomic Feature ◽  
Reduced Representation ◽  
Standard Set ◽  
Selection Of ◽  
Page Electrophoresis

Reduced representation sequencing is a practical approach for obtaining genetic variations from a random subsample of the genome. RADseq (Restriction Site-Associated DNA Sequencing), as one of the more popular reduced representation approaches, is currently being used in a wide array of applications including marker development, phylogenetics, and population genomics. A crucial step in designing a RADseq experiment is the selection of one or a pair of restriction enzymes (RE) that will result in sufficient density of loci to meet the objectives of the study, which is not straightforward because of difficulties in obtaining a standard set of REs that can generally be applied to RADseq experimental designs. Here we present RApyDS, a simulation tool that provides users with evaluation metrics to aid in choosing suitable REs based on their target RADseq design. RApyDS can perform simulations for single- or double-digest RADseq, preferably with a supplied reference genome. The tool outputs an overview page, electrophoresis visualization, mapping of restriction cut sites, and RAD loci density across the genome. If supplied with an annotation file, the program can also output evaluation metrics for a specified genomic feature. The tool is currently available at https://github.com/pgcbioinfo/rapyds.

scholarly journals Derived Polymorphic Amplified Cleaved Sequence (dPACS): A Novel PCR-RFLP Procedure for Detecting Known Single Nucleotide and Deletion–Insertion Polymorphisms

2019 ◽  
Vol 20 (13) ◽  
pp. 3193 ◽  
Author(s):  
Shiv Shankhar Kaundun ◽  
Elisabetta Marchegiani ◽  
Sarah-Jane Hutchings ◽  
Ken Baker
Keyword(s):  
Gel Electrophoresis ◽  
Restriction Site ◽  
Restriction Enzymes ◽  
Nucleotide Polymorphisms ◽  
Acetyl Coa Carboxylase ◽  
Wild Type ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Broadleaf Species ◽  
Selection Of

Most methods developed for detecting known single nucleotide polymorphisms (SNP) and deletion–insertion polymorphisms (DIP) are dependent on sequence conservation around the SNP/DIP and are therefore not suitable for application to heterogeneous organisms. Here we describe a novel, versatile and simple PCR-RFLP procedure baptised ‘derived Polymorphic Amplified Cleaved Sequence’ (dPACS) for genotyping individual samples. The notable advantage of the method is that it employs a pair of primers that cover the entire fragment to be amplified except for one or few diagnostic bases around the SNP/DIP being investigated. As such, it provides greater opportunities to introduce mismatches in one or both of the 35–55 bp primers for creating a restriction site that unambiguously differentiates wild from mutant sequences following PCR-RFLP and horizontal MetaPhorTM gel electrophoresis. Selection of effective restriction enzymes and primers is aided by the newly developed dPACS 1.0 software. The highly transferable dPACS procedure is exemplified here with the positive detection (in up to 24 grass and broadleaf species tested) of wild type proline106 of 5-enolpyruvylshikimate-3-phosphate synthase and its serine, threonine and alanine variants that confer resistance to glyphosate, and serine264 and isoleucine2041 which are key target-site determinants for weed sensitivities to some photosystem II and acetyl-CoA carboxylase inhibiting herbicides, respectively.

scholarly journals PERTUMBUHAN DAN VARIASI GENETIK IKAN BANDENG, Chanos chanos DARI PROVINSI ACEH, BALI, DAN GORONTALO, INDONESIA

2018 ◽  
Vol 12 (4) ◽  
pp. 307 ◽  
Author(s):  
Sari Budi Moria Sembiring ◽  
Gigih Setia Wibawa ◽  
Tony Setiadharma ◽  
Haryanti Haryanti
Keyword(s):  
Genetic Variation ◽  
Cytochrome B ◽  
Restriction Site ◽  
Seed Quality ◽  
Restriction Enzymes ◽  
International Markets ◽  
Chanos Chanos ◽  
Dna Analyses ◽  
Important Fish ◽  
Selection Of

Ikan bandeng, Chanos chanos merupakan salah satu ikan ekonomis penting di Asia. Sejak tahun 1995, di Indonesia sebagian besar benih bandeng diproduksi dari hatchery sekitar Dusun Gondol, Bali Utara baik untuk pasar domestik maupun perdagangan internasional. Dalam rangka meningkatkan kualitas benih, perlu dilakukan perbaikan induk secara genetik menggunakan populasi yang unggul. Tujuan penelitian ini adalah mendapatkan data laju pertumbuhan dan variasi genetik induk ikan bandeng yang berasal dari lokasi perairan Aceh, Bali, dan Gorontalo. Pertumbuhan ikan bandeng diamati melalui pengukuran panjang dan bobot benih hingga ukuran 500 g (calon induk), serta variasi genetik diamati menggunakan metode RFLP DNA. Benih dan calon induk masing-masing dianalisis sebanyak 15 ekor. Hasil pengamatan pertumbuhan ikan bandeng mulai dari benih hingga menjadi calon induk, menunjukkan bahwa ikan bandeng dari Aceh dan Bali mempunyai pertumbuhan panjang dan bobot yang relatif lebih tinggi dibandingkan dengan ikan bandeng dari Gorontalo, walaupun secara statistik tidak berbeda nyata (P<0,05). Hasil analisis variasi genetik terdapat lima komposit haplotipe dari empat enzim restriksi yaitu Mbo I, Hae III, Hha I, dan Nla IV pada sekuens cytochrome-b. Jumlah rata-rata restriction site adalah 1-3 haplotipe. Populasi Aceh dan Bali memiliki nilai keragaman genetik yang lebih rendah (0,080 dan 0,000) dibandingkan dengan calon induk dari benih Gorontalo (0,115).Milkfish, Chanos chanos is one of the economically important fish in Asia. Since 1995, milkfish seed mostly produced in Gondol area, Northern part of Bali, and suppleted both domestic and international markets. In order to improve its seed quality the improvement of milkfish broodstock genetic is required through selection of superior population. The aims of this research were to evaluate the growth performance and genetic variation of milkfish populations from Aceh, Bali, and Gorontalo Province. The length and weight of fry up to 500 g was measured as well as the genetic variation was detected using RFLP DNA method. Fry and young broodstock in the DNA analyses were 15 individuals. The results showed that the growth in length and weight milkfish seed from fry to young broodstock (size up to 500 g) from Aceh and Bali was slightly higher than that of Gorontalo, but no significant differences (P>0.05) were observed among the populations. The genetic analysis showed five haplotypes composite from four restriction enzymes i.e., Mbo I, Hae III, Hha I, and Nla IV at on cytochrome-b sequen. The average number of restriction site was 1-3 haplotypes. Aceh and Bali populations have lower genetic variations (0.080 and 0.000) compared to Gorontalo (0.115).

Hereditary predisposition to breast cancer and its relation to the BRCA1 and BRCA2 genes: literature review

2018 ◽  
Vol 50 (1) ◽  
Author(s):  
Aline Silva Coelho ◽  
Marielle Anália da Silva Santos ◽  
Rosecleide Inácio Caetano ◽  
Camila Fátima Piovesan ◽  
Larissa Aparecida Fiuza ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Literature Review ◽  
Brca1 And Brca2 ◽  
Hereditary Predisposition ◽  
Brca1 And Brca2 Genes

scholarly journals Comparative In Vitro and In Silico Analyses of Variants in Splicing Regions of BRCA1 and BRCA2 Genes and Characterization of Novel Pathogenic Mutations

PLoS ONE ◽  
2013 ◽  
Vol 8 (2) ◽  
pp. e57173 ◽  
Author(s):  
Mara Colombo ◽  
Giovanna De Vecchi ◽  
Laura Caleca ◽  
Claudia Foglia ◽  
Carla B. Ripamonti ◽  
...  
Keyword(s):  
In Silico ◽  
Brca1 And Brca2 ◽  
Pathogenic Mutations ◽  
Brca1 And Brca2 Genes ◽  
In Silico Analyses

Genetic testing for BRCA1 and BRCA2 genes

2014 ◽  
Vol 39 (6) ◽  
pp. 8-10
Author(s):  
Cathy R. Kessenich ◽  
Kathryn Bacher ◽  
Patricia A. Moore
Keyword(s):  
Genetic Testing ◽  
Brca1 And Brca2 ◽  
Brca1 And Brca2 Genes

A workflow for the detection and classification of variants in the BRCA1 and BRCA2 genes

Pathology ◽  
2016 ◽  
Vol 48 ◽  
pp. S96
Author(s):  
Sarah L. Nickerson ◽  
Stella W.S. Lai ◽  
Rongying Tang ◽  
Debra O. Prosser ◽  
Donald R. Love
Keyword(s):  
Brca1 And Brca2 ◽  
Brca1 And Brca2 Genes

scholarly journals Identification of restriction enzyme in the FSHR gene of indonesian local cattle

2021 ◽  
Vol 888 (1) ◽  
pp. 012024
Author(s):  
P W Prihandini ◽  
A Primasari ◽  
M Luthfi ◽  
D Pamungkas ◽  
A P Z N L Sari ◽  
...  
Keyword(s):  
Restriction Enzyme ◽  
Restriction Site ◽  
Follicle Stimulating Hormone ◽  
Restriction Enzymes ◽  
Future Studies ◽  
Fshr Gene ◽  
Pcr Rflp ◽  
Mapping Analysis ◽  
Pcr Products ◽  
Enzyme Mapping

Abstract The restriction enzyme is important for genotyping using the PCR-RFLP technique. Therefore, this study aims to identify the restriction enzyme mapping in the partial sequence of the follicle-stimulating hormone receptor (FSHR) gene in Indonesian local cattle. A total of 29 samples sized 306 bp, were aligned with Genbank sequence acc no. NC_032660, resulting three polymorphic sites, namely g.193G>C, g.227T>C, and g.275A>C. Furthermore, the restriction mapping analysis using the NEBcutter program V2.0 showed that no enzyme recognized the SNP g.275A>C, while the SNP g.193G>C and g.227T>C were identified by the AluI and MscI enzymes, respectively. The AluI enzyme cuts at two positions (193 bp and 243 bp) in the G allele sample producing three fragments namely 50 bp, 63 bp, and 193 bp, meanwhile, in the C allele, the AluI cuts only in position 243 bp, hence, the fragment products are 63 bp and 243 bp. In contrast, the MscI enzyme was only recognized in the T allele, producing fragments sized 77 bp and 229 bp but failed to identify the restriction site along with the PCR products in the C allele. Based on the results, the SNPs (g.193G>C and g.227T>C) and restriction enzymes (AluI and MscI) are applicable for genotyping local Indonesian cattle using the PCR-RFLP technique in future studies.

scholarly journals MUTATIONS IN BRCA1 AND BRCA2 GENES AS A CAUSE OF HEREDITARY BREAST CANCER

2020 ◽  
Vol 13 (4) ◽  
pp. 39-43
Author(s):  
REGINA R. GIMAEVA ◽  
◽  
ELENA A. KUPRIYANOVA ◽  
DENIS I. GABELKO ◽  
◽  
...  
Keyword(s):  
Breast Cancer ◽  
Hereditary Breast Cancer ◽  
Brca1 And Brca2 ◽  
Brca1 And Brca2 Genes
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