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However, current HLA DNA typing methods especially for HLA-DRB1 generally yielded ambiguous typing results because of high degree of heterozygosity on exome region and primer pairs design limitations, which generally amplified only exon2 of HLA-DRB1 and the position of its primer pairs is on exome region.
Forensic DNA casework samples are often of insufficient quantity or quality to generate full profiles by conventional DNA typing methods.
DNA typing methods have emerged as more practical and reliable option for the investigation of outbreaks.
A protocol and case report forms were developed to standardize methodology for case ascertainment, specimen and data collection, and DNA typing methods.
Therefore, simplification, acceleration and cost-saving in the NGS protocols are required if they are to become routine DNA typing methods and replace the conventional HLA genotyping methods such as SBT and PCR-SSOP (e.g. Luminex methodology).
At present, most DNA typing methods for species determination are based on PCR amplification using species-specific primers for single species.
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Super high resolution-single molecule-sequence-based typing (SS-SBT) is an HLA DNA typing method to the field 4 level of allelic resolution (8-digit typing) by combination of long ranged PCR amplification and next generation sequencing (NGS) technologies.
FLiP is a DNA typing method for M. tuberculosis complex strains described by Reisig et al. in 2005 [ 16].
HLA low to intermediate typing was performed by One Lambda LABType reverse SSO Luminex DNA typing method (One Lambda, Canoga Park, CA, USA).
The HLA class II genes were genotyped using the LABType® SSO which applies Luminex® technology to the reverse sequence-specific oligonucleotide (SSO) DNA typing method.
Other methods for M. africanum identification, such as by real-time PCR, microarray analysis, and spoligotyping (a DNA typing method) may also present advantages to laboratories with these capabilities, but these modalities were not evaluated in the current study.
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