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For example, genome-wide association studies have identified SNPs associated with diseases such as rheumatoid arthritis [8] and prostate cancer. [9] A SNP array can also be used to generate a virtual karyotype using software to determine the copy number of each SNP on the array and then align the SNPs in chromosomal order.
In human genetics, a human Y-chromosome DNA haplogroup is a haplogroup defined by specific mutations in the non-recombining portions of DNA on the male-specific Y chromosome (Y-DNA). Individuals within a haplogroup share similar numbers of short tandem repeats (STRs) and single-nucleotide polymorphisms (SNPs). [ 2 ]
Geneticist Spencer Wells suggests that haplogroup K likely originated in the Middle East or Central Asia, perhaps in the region of Iran or Pakistan. [6] According to Bergstorm et al, deep-rooted haplogroup K2b1 (Y-haplogroup S/M) found in Indigenous Australians and ancestors of haplogroup R and Q (Y-haplogroup K2b2/root P) split in Southeast Asia near Sahul. [8]
Optical mapping [1] is a technique for constructing ordered, genome-wide, high-resolution restriction maps from single, stained molecules of DNA, called "optical maps". By mapping the location of restriction enzyme sites along the unknown DNA of an organism, the spectrum of resulting DNA fragments collectively serves as a unique "fingerprint" or "barcode" for that sequence.
In the field of genetic sequencing, genotyping by sequencing, also called GBS, is a method to discover single nucleotide polymorphisms (SNP) in order to perform genotyping studies, such as genome-wide association studies . [1] GBS uses restriction enzymes to reduce genome complexity and genotype multiple DNA samples. [2]
Common challenges of DNA sequencing with the Sanger method include poor quality in the first 15–40 bases of the sequence due to primer binding and deteriorating quality of sequencing traces after 700–900 bases. Base calling software such as Phred typically provides an estimate of quality to aid in trimming of low-quality regions of sequences.
Sequencing by ligation (SOLiD sequencing) 50+35 or 50+50 bp: 99.9%: 1.2 to 1.4 billion: 1 to 2 weeks: $60–130: Low cost per base. Slower than other methods. Has issues sequencing palindromic sequences. [109] Nanopore Sequencing: Dependent on library preparation, not the device, so user chooses read length (up to 2,272,580 bp reported [110 ...
The complexity of sequence assembly is driven by two major factors: the number of fragments and their lengths. While more and longer fragments allow better identification of sequence overlaps, they also pose problems as the underlying algorithms show quadratic or even exponential complexity behaviour to both number of fragments and their length.