SBT Unique Selling Points

Slides:

Advertisements

Similar presentations

Diagnosis with PCR This is a preparation of DNA. We zoomed in a portion of a gene. We know that two primers, Forward and Reverse, will hybridize at specific.

Advertisements

Considerations for Analyzing Targeted NGS Data HLA

HLA: matching and donor selection

C4 long gene (20.4kb) C4 short gene (14.1kb) HERV-K(C4) Exon26, amino acids C4B gene C4A gene PCPVLD GGGGGGACAACAGGTCACAATCTGCTG.

Introduction  Human leukocyte antigen (HLA) is the major histocompatibility complex (MHC) in humans  Group of genes ('superregion') on chromosome 6.

HLA Genotyping Data Generated by 454 Sequencing Cherie Holcomb, Ph.D. Roche Molecular Systems picture placeholder NGS Data Consortium October 8, 2012.

HLA Analysis and Next Generation Sequencing Henry Erlich, Ph.D. Cherie Holcomb, Ph.D. Roche Molecular Systems picture placeholder NGS and EFI, May 14,

Remember the limitations? –You must know the sequence of the primer sites to use PCR –How do you go about sequencing regions of a genome about which you.

PCR amplification of ovine somatotropin gene and its partial characterization Moazzam Ali & Dr. Waheed Akhtar.

Chapter 6 PCR and in vitro Mutagenesis A. Basic features of PCR 1. PCR is a cell-free method of DNA cloning standard PCR reaction is a selective DNA amplification.

Fig. S1 Mass spectra analysis of XXT4 reaction products demonstrating xylosyltransferase activity towards cellohexaose substrate. Predominant peaks represent.

PCR Y.Martinez, LSHS, 2014 DIRECTIONS: COPY NOTES IN ORANGE.

Assay I HLA-DQ Alpha (A1) Haplotype. Purpose To determine which one of several known alleles is present at the HLA DQ α locus on each of an individual’s.

Validation of HLA Typing by NGS

Anajane G. Smith1, 2 Shalini E. Pereira1, 2 Dan E. Geraghty1, 2

16-point HLA Typing with Long Amplicon Analysis v2

All rights Reserved Cengage/NGL/South-Western © 2016.

Implementation Insights

New NGS products.

Introduction to GENDX HLA typing products

Causes of Variation in Substitution Rates

MAJOR HISTOCOMPATIBILITY COMPLEX

Major Histocompatibility Complex

All rights Reserved Cengage/NGL/South-Western © 2016.

HLA typing disease association and transplantation

Alu insert, PV92 locus, chromosome 16

DNA Analysis of the HLA Gene Complex

Figure 2 Analysis of restriction sites that define the 5′ and 3′ boundaries of the region of identity between RHD and the Ce allele. TaqI (a) and HinfI.

Recurrent inversion breaking intron 1 of the factor VIII gene is a frequent cause of severe hemophilia A by Richard D. Bagnall, Naushin Waseem, Peter M.

Chapter 4 “DNA Finger Printing”

Polymerase Chain Reaction

Major Histocompatibility complex OR

Resolving Ambiguities

Vav‐1 gene‐targeting strategy.

Alternative Splicing of a Novel Glycophorin Allele GPHe(GL) Generates Two Protein Isoforms in the Human Erythrocyte Membrane by Cheng-Han Huang, Olga O.

RHD gene deletion occurred in the Rhesus box

بنام خداي زيبائيها.

Major Histocompatibility Complex

Performance Characteristics and Validation of Next-Generation Sequencing for Human Leucocyte Antigen Typing Eric T. Weimer, Maureen Montgomery, Rosanne.

Bertram et al. (2005) , NEJM, 352: Bertram et al. (2005) , NEJM, 352:

Richard G. Phelps, Andrew J. Rees Kidney International

HLA-Class I: Typing Theory

Molecular Diagnosis of Autosomal Dominant Polycystic Kidney Disease Using Next- Generation Sequencing Adrian Y. Tan, Alber Michaeel, Genyan Liu, Olivier.

HLA-DM gene polymorphisms in atopic dermatitis

Hou-Sung Jung, Gregory J. Tsongalis, Joel A. Lefferts

Homozygous Deletion of the Very Low Density Lipoprotein Receptor Gene Causes Autosomal Recessive Cerebellar Hypoplasia with Cerebral Gyral Simplification

The Molecular Basis of Focal Cyst Formation in Human Autosomal Dominant Polycystic Kidney Disease Type I Feng Qian, Terry J Watnick, Luiz F Onuchic,

Andrea Gaedigk, Amanda K. Riffel, J. Steven Leeder

Mapping MHC-Resident Transplantation Determinants

Catherine E. Keegan, Anthony A. Killeen

Supplemental Figure 3 A B C T-DNA 1 2 RGLG1 2329bp 3 T-DNA 1 2 RGLG2

Molecular cloning of pms916 salt hypersensitive T-DNA mutant.

Validation and Clinical Application of a Locus-Specific Polymerase Chain Reaction- and Minisequencing-Based Assay for Congenital Adrenal Hyperplasia (21-Hydroxylase.

Structure of the GM2A Gene: Identification of an Exon 2 Nonsense Mutation and a Naturally Occurring Transcript with an In-Frame Deletion of Exon 2 Biao.

Volume 65, Issue 6, Pages (June 2004)

Comprehensive Mutation Analysis of the CYP21A2 Gene

GT repeats are unique to Cdk6 and are conserved in different mammals.

A Multi-Exonic BRCA1 Deletion Identified in Multiple Families through Single Nucleotide Polymorphism Haplotype Pair Analysis and Gene Amplification with.

Marija Debeljak, Donald N. Freed, Jane A

Heterozygous for all alleles in MHC II

Features & Benefits GENDX SBT Products

WRKY20 dual sgRNA approach.

DNA Profiling Vocabulary

Genomic structure of LTBP-4 around the 3rd 8-Cys repeat.

Genotyping the intron 22 XbaI A restriction fragment length polymorphism (RFLP) using long distance PCR (LD-PCR). Genotyping the intron 22 XbaI A restriction.

Genotype analysis of the neuropeptide Y (NPY) Y1 and NPY Y5 receptor genes in gonadotropin-releasing hormone–dependent precocious gonadarche Mandi Barker-Gibb,

Bicuspid aortic valve and ascending aortic aneurysm are not associated with germline or somatic homeobox NKX2-5 gene polymorphism in 19 patients Ramanath.

Figure Genetic characterization of the novel GYG1 gene mutation (A) GYG1_cDNA sequence and position of primers used. Genetic characterization of the novel.

Fang Wang, Yunfeng Wang, Jie Ding, Jiyun Yang Kidney International

Presentation transcript:

SBT Unique Selling Points

SBTexcellerator® Single PCR reaction per HLA locus For HLA Class I coverage of the complete gene For HLA class II coverage of exon 2 (and exon3) Primers provided for amplification and sequencing Core regions Extended regions to resolve allele ambiguities GSSP’s to resolve genotype ambiguities 2

Amplification strategy HLA-A (3.1 kb) 1 8 7 6 5 4 3 2 UTR HLA-B (3.4 kb) HLA-C (3.4 kb) HLA-DRB1 (3.7-4.8 kb) HLA-DQB1 (3.7-4.1 kb) HLA-DPB1 (5.0 & 5.7 kb) HLA-DPA1 (4.7 kb) HLA-DQA1 (5.4-5.8 kb) HLA-DRB3 (3.8 kb) HLA-DRB4 (0.4 & 1.3 kb) HLA-DRB5 (4.0 kb) SBTexcellerator amplification primer Amplified exon Exon not amplified Class I amplified entirely Class II large introns, not all exons amplified.

Reagent Box Set-up 2 3 4 5 6 7 8 3’UTR 1 5’UTR CORE EXTENDED FULL 4

SBTexcellerator® High priority regions (intron positions) exclude null alleles GPS tool resolving genotype ambiguities to speed up the process Highest number of GSSP’s per locus Resolving utmost all genotype ambiguities Development/manufacturer of reagents en software under 1 roof Highest level and fast support