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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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,...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Point and Frameshift Mutations01:30

Point and Frameshift Mutations

Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...

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Updated: Jun 22, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Multiplex padlock targeted sequencing reveals human hypermutable CpG variations.

Jin Billy Li1, Yuan Gao, John Aach

  • 1Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. jli@genetics.med.harvard.edu

Genome Research
|June 16, 2009
PubMed
Summary
This summary is machine-generated.

This study significantly improved padlock capture technology for next-generation sequencing, enabling efficient identification of genetic variations in human chromosome 21

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Area of Science:

  • Genomics
  • Molecular Biology
  • Human Genetics

Background:

  • Next-generation sequencing requires efficient multiplex enrichment of genomic loci.
  • Existing technologies need substantial improvements for large-scale applications.

Purpose of the Study:

  • To report a 10,000-fold improvement in a padlock-based enrichment approach.
  • To apply this enhanced assay for identifying genetic variations in human chromosome 21's hypermutable CpG regions.

Main Methods:

  • Utilized an improved padlock capture method for targeted enrichment.
  • Applied Illumina sequencing to analyze approximately 50,500 target sites across human chromosome 21.
  • Determined alleles at over 400,000 target base positions in six subjects.

Main Results:

  • Achieved 94% target site observation with high coverage uniformity (93% within 100-fold, 57% within 10-fold).
  • High concordance (98.4%-100%) with independent genotypes.
  • Discovered over 500 novel single nucleotide polymorphisms (SNPs), with 362 in targeted CpG locations.
  • Observed CpG transitions were 13.7 times more abundant than non-CpG transitions.

Conclusions:

  • The enhanced padlock capture technology enables efficient, large-scale multiplex enrichment for next-generation sequencing.
  • Targeted CpG resequencing is effective for identifying common and rare genetic variations.
  • Methylation rate heterogeneity may contribute to mutation rate variation in humans.