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The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the nuclear genome and the mitochondrial genome. Human genomes include both protein-coding DNA genes and noncoding DNA. Haploid human genomes, which are contained in germ cells consist of three billion DNA base pairs, while diploid genomes have twice the DNA content. While there are significant differences among the genomes of human individuals, these are considerably smaller than the differences between humans and their closest living relatives, the bonobos and chimpanzees.
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.
Sanger sequencing is a method of DNA sequencing based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication. After first being developed by Frederick Sanger and colleagues in 1977, it became the most widely used sequencing method for approximately 40 years. It was first commercialized by Applied Biosystems in 1986. More recently, higher volume Sanger sequencing has been replaced by "Next-Gen" sequencing methods, especially for large-scale, automated genome analyses. However, the Sanger method remains in wide use, for smaller-scale projects, and for validation of Next-Gen results. It still has the advantage over short-read sequencing technologies in that it can produce DNA sequence reads of > 500 nucleotides.
A Phred quality score is a measure of the quality of the identification of the nucleobases generated by automated DNA sequencing. It was originally developed for Phred base calling to help in the automation of DNA sequencing in the Human Genome Project. Phred quality scores are assigned to each nucleotide base call in automated sequencer traces. The FASTQ format encodes phred scores as ASCII characters alongside the read sequences. Phred quality scores have become widely accepted to characterize the quality of DNA sequences, and can be used to compare the efficacy of different sequencing methods. Perhaps the most important use of Phred quality scores is the automatic determination of accurate, quality-based consensus sequences.
Probable G-protein coupled receptor 22 is a protein that in humans is encoded by the GPR22 gene.
Integral membrane protein GPR155, also known as G protein-coupled receptor 155, is a protein that in humans is encoded by the GPR155 gene. Mutations in this gene may be associated with autism.
Probable G-protein coupled receptor 85 is a protein that in humans is encoded by the GPR85 gene.
Bardet–Biedl syndrome 5 protein is a protein that in humans is encoded by the BBS5 gene.
Ubiquitin-like modifier-activating enzyme 6 is a protein that in humans is encoded by the UBA6 gene.
Zinc finger protein 655 is a protein that in humans is encoded by the ZNF655 gene.
39S ribosomal protein L19, mitochondrial is a protein that in humans is encoded by the MRPL19 gene.
WD repeat and FYVE domain-containing protein 3 is a protein that in humans is encoded by the WDFY3 gene.
AP-1 complex-associated regulatory protein is a protein that in humans is encoded by the AP1AR gene.
Transmembrane protein 150A is a protein that, in humans, is encoded by the TMEM150A gene.
Poly [ADP-ribose] polymerase 12 is an enzyme that in humans is encoded by the PARP12 gene.
Putative ATP-dependent RNA helicase DHX57 is an enzyme that in humans is encoded by the DHX57 gene.
Methylmalonic aciduria and homocystinuria type D protein, mitochondrial also known as MMADHC is a protein that in humans is encoded by the MMADHC gene.
Phred base calling is a computer program for identifying a base (nucleobase) sequence from a fluorescence "trace" data generated by an automated DNA sequencer that uses electrophoresis and 4-fluorescent dye method. When originally developed, Phred produced significantly fewer errors in the data sets examined than other methods, averaging 40–50% fewer errors. Phred quality scores have become widely accepted to characterize the quality of DNA sequences, and can be used to compare the efficacy of different sequencing methods.
Philip Palmer Green is a theoretical and computational biologist noted for developing important algorithms and procedures used in Gene mapping and DNA sequencing. He earned his doctorate from Berkeley in mathematics in 1976 with a dissertation on C*-algebra under the direction of Marc Rieffel, but transitioned from pure mathematics into applied work in biology and bioinformatics. Green has obtained numerous important results, including in developing Phred, a widely used DNA trace analyzer, in mapping techniques, and in genetic analysis. Green was elected to the National Academy of Sciences in 2001 and won the Gairdner Award in 2002.
Michael Christopher Wendl is a mathematician and biomedical engineer who has worked on DNA sequencing theory, covering and matching problems in probability, theoretical fluid mechanics, and co-wrote Phred. He was a scientist on the Human Genome Project and has done bioinformatics and biostatistics work in cancer. Wendl is of ethnic German heritage and is the son of the aerospace engineer Michael J. Wendl.
References
- ↑ Wenz, C (2005) Author Profile: Ladeana Hillier. Nurture 1, pp. 2.
- ↑ Sulston, J and Ferry, G (2002) The Common Thread: A Story of Science, Politics, Ethics, and the Human Genome, Joseph Henry Press.
- ↑ Hillier, LW et al. (2003) The DNA sequence of human chromosome 7. Nature 424(6945), 157–164.
- ↑ Hillier, LW et al. (2005) Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature 434(7034), 724–731.
- ↑ Hillier, LW et al. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432(7018), 695–716.
- ↑ Hillier, LW et al. (2008) Whole-genome sequencing and variant discovery in C-elegans. Nature Methods 5(2), 183–188.
- ↑ Hillier, LW et al. (1996) Generation and analysis of 280,000 human expressed sequence tags. Genome Research 6(9), 807–828.
- ↑ Ewing, B., Hillier, L., Wendl, M.C., and Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Research 8(3), 175–185. PMID 9521921 full article
- ↑ Koboldt, D. C. and Miller, R. D. (2011) Identification of Polymorphic Markers for Genetic Mapping, chapter 2 in "Genomics: Essential Methods", John Wiley and Sons.
- ↑ Highsmith, W. E. (2006) Electrophoretic Methods for Mutation Detection and DNA Sequencing, chapter 9 in "Molecular Diagnostics for the Clinical Laboratorian", Humana Press
