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Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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An integrated Asian human SNV and indel benchmark established using multiple sequencing methods.

Chuanfeng Huang1, Libin Shao2, Shoufang Qu1

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Researchers developed a high-confidence Asian human genome variation benchmark using a Chinese Han cell line. This benchmark, generated with diverse sequencing strategies, aids precision medicine by providing accurate genetic variation data for Asian populations.

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Area of Science:

  • Genomics
  • Clinical Diagnostics
  • Bioinformatics

Background:

  • Advancements in sequencing technologies drive clinical diagnosis.
  • Accurate genome variation benchmarks are crucial for precision medicine.
  • A population-specific variation benchmark for Asian populations is currently lacking.

Purpose of the Study:

  • To establish an Asian human variation benchmark.
  • To provide a high-confidence reference for genetic variation in an Asian population.
  • To support the development of sequencing-based clinical applications.

Main Methods:

  • Construction and sequencing of a stabilized Chinese Han cell line.
  • Utilizing seven diverse sequencing strategies and multiple analysis pipelines.
  • Employing long-read sequencing technologies (stLFR and PacBio HiFi CCS) for phasing.

Main Results:

  • Identification of 3.35 million single nucleotide variants (SNVs) and 348.65 thousand insertions/deletions (indels).
  • Detection of 5,913 high-quality SNVs, including 969 novel variants in homologous regions.
  • Phasing of over 99% of heterozygous SNVs to the haplotype level.

Conclusions:

  • The study provides a comprehensive Asian human variation benchmark.
  • This benchmark is valuable for future sequencing-based clinical development in Asian populations.
  • The integrated data enhances the accuracy of genome variation detection and precision medicine.