Synaptic change in PD
110, changing it to a codon for Glutamine (Gln, Q) and adding a tail of new amino acids to the protein’s C-terminus ending at a new stop codon (Ter17/*17)
- date 2012-11-01 p.*32/Argext*? (alternatively p.Ter32ArgextTer? or p.*32/Rext?) describes a variant in the stop codon at position 327, changing it to a codon for Arginine (Arg, R) and adding a tail of new amino acids of unknown length since the shifted frame does not contain a new stop codon (see FAQ).
More changes in one individual
Two or more changes in one individual are described by combining the changes, per chromosome (maternal and paternal), between square brackets (”[ ; ; / ; / ; / ]”) and using a semicolon (”;”) as separator: [first change maternal; second change maternal] ; [first change paternal; second change paternal]. When changes are in different genes on different chromosomes a space (” ”) is used to separate the different chromosomes (”[ ; / ; / ]”).
- Two changes in one gene on one chromosome
- deriving from two independent changes at DNA level are described as “[first change;second change]” (see Discussion).
- p.[(Ala25Thr; Gly28Val)] indicates two predicted changes derived from one chromosome (RNA or protein not analysed); predicted change amino acid Alanine25 to Threonine and Glycine-28 to Valine
- deriving from one change at DNA level that has more than one effect on RNA/protein level are described as “[first change, second change]” (see Discussion).
- p.[Asn26His, Ala25_Gly29del] describes two protein changes deriving from one change on a chromosome (c.76A>C at DNA level) resulting in two transcripts (RNA level r.[76a>c, 73_88xdel]) yielding two predicted proteins, one where amino acid Asparagine25 changes to Histidine and one with a deletion of amino acids Asparagine25 to Glycine29
- deriving from two independent changes at DNA level are described as “[first change;second change]” (see Discussion).
- Two changes in one gene on different chromosomes (e.g. in recessive diseases)
- p.[Ala25Thr];[Gly28Val] describes two changes derived from a gene on each chromosome (one paternal, one maternal); predicted change amino acid Alanine25 to Threonine on one chromosome and Glycine28 to Valine on the other chromosome (RNA or protein not analysed)
- Examples
- p.[(Ala25Thr)];[(Gly28Val)] describes two changes derived from one gene on each chromosome (one paternal, one maternal); predicted change amino acid Alanine25 to Threonine on one chromosome and Glycine28 to Valine on the other chromosome (RNA or protein not analysed)
- NOTE: the description p.([Ala25Thr];[Gly28Val]) should not be used
- p.[Ala25Thr];[(Pro323Leu)] described a predicted change of amino acid Alanine25 to Threonine derived from one chromosome (RNA or protein analysed) and Proline323 to Leucine derived from the other chromosome (RNA or protein not analysed)
- p.[Ala25Thr];[?] describes a change of amino acid Alanine25 to Threonine derived from one chromosome and an unknown change derived from the other (RNA or protein not analysed)
- NOTE: “unknown change in the other allele” does not only mean that no DNA-change was detected in the other chromosome but includes cases where the consequence of a detected change is unclear or can not be predicted (e.g. the consequence of a change at the splice site)
- p.[Ala25Thr];[=] denotes a change of amino acid Alanine25 to Threonine derived from one chromosome and a normal sequence (indicated by ”=”) of the other chromosome (see FAQ)
- p.[(Ala25Thr)];[(Gly28Val)] describes two changes derived from one gene on each chromosome (one paternal, one maternal); predicted change amino acid Alanine25 to Threonine on one chromosome and Glycine28 to Valine on the other chromosome (RNA or protein not analysed)
- Two sequence changes in one gene with chromosomes unknown are described as “[change 1(;)change 2]” (see Disucssion).
- p.[(Ala25Thr)(;)(Pro323Leu)] describes that two changes were identified in one individual (amino acid Alanine25 to Threonine and Proline323 to Leucine, RNA or protein analysed), but it is not known whether these changes are on the same chromosome (in cis) or on different chromosomes (in trans)
- p.[(Ala25Thr)(;)(Pro323Leu)] describes that two changes were identified in one individual (amino acid Alanine25 to Threonine and Proline323 to Leucine, RNA nor protein analysed), but it is not known whether these changes are on the same chromosome (in cis) or on different chromosomes (in trans). Alternatively p.[(Ala25Thr)(;)(Pro323Leu)] can be used.
- NEW Mosaicism is described using ”/”
- p.[Arg83=/Arg83Ser] describes a somatic case where a chromosome in some cells contains a normal sequence (p.Arg83=), while other cells contain a Ser at this position (p.Arg83Ser)
- NEW Chimerism is described using ”//”
- p.[Arg83=//Arg83Ser] describes a chimeric organism where a chromosome in some cells contain a normal sequence (Arg83=), while other cells contain anotehr chromosome with Ser at this position (p.Arg83Ser)
fathmm prediction pathogenic score
- A high-throughput web-server capable of predicting the functional consequences of missense mutation
- both coding variants, i.e. non-synonymous single nucleotide variants (nsSNVs), and non-coding variants in the human genome.
- he functional scores for individual mutations from FATHMM-MKL are in the form of a single p-value, ranging from 0 to 1. Scores above 0.5 are deleterious, but in order to highlight the most significant data in COSMIC, only scores ≥ 0.7 are classified as ‘Pathogenic’. Mutations are classed as ‘Neutral’ if the score is ≤ 0.5.
Genotyping Methods
| 기존에 이미 알고 있는 마커들을 디자인해서 보는 방법 | Sequencing (= 전장 유전체 혹은 한 유전자 내 전체 염기를 순서대로 보는 방식) | ||||
|---|---|---|---|---|---|
| TaqMan | microarray | Sanger Sequencing (= "chain termination method") (a type of direct sequencing) | Next Generation Sequencing (DNA 서열 증폭 → 형광 표식 등을 카메라로 찍어 이미지를 처리하는 과정을 거쳐 염기를 읽어낸다) | ||
| Roche, 454 life Science (최초) | Illumina / Oxford Nano | ||||
| principle | 보고자 하는 부위의 SNP 염기에 대응하는 프로브(probe) 끝에 형광물질인 FAM 혹은 VIC를 붙인 후 형광판독기를 통해 나타나는 형광색을 읽는 방식으로 SNP를 판독하는 방법이다. 384개의 웰(well)로 구성된 플레이트부터 최근에 보편적으로 사용되는 3072개 웰(well)을 갖춘 플레이트에 이르기까지 해당 플레이트에 원하는 프로브를 집어 넣어서 대량으로 보고싶은 SNP를 지노타이핑 하는 방식이다. | = DNA chip, Biochip, gene-array, 분석하고자 하는 유전자를 잘라내 형광물질을 입힌 다음, DNA 칩 위에 액체형태로 바른다. DNA 칩과 분석대상인 유전자에 남신 구성요소들이 A와 T, G와 C처럼 서로 짝을 찾아 결합한다. 그 위에 레이저 빛을 쏘이면 결합유전자들은 밝은 빛을 낸다. 이 과정을 반복해 발광 위치를 확인하면 분석대상 유전자의 염기서열을 알 수 있다. | A,T,G,C 염기의 분자량(molecular weight)의 차이를 전기영동 시킨 후 레이저 빛을 각 전기영동 밴드에 쬐면 형광물질에 따라 특이적인 파장의 빛을 발하게 되며, 이를 순서대로 읽어내 각 염기를 읽어내는 방식이다. In Sanger sequencing, the obtained sequencing reads are an average of all DNA present in the PCR mixture. | 전체 유전자를 200여 개의 크기로 구성된 염기 조각으로 나누고, 잘게 나눈 각각의 조각을 읽어낸 후 그를 한 줄로 이어 원래 30억 개 규모의 전체 유전코드로 재구성하는 방식이다. 이런 방식은 Sanger 방식과 달리 대량의 병렬 데이터 생산이 가능 | |
| result | 일부적 | 수십-수백개 마커 | 질병관리본부의 한국인 칩 프로젝트에서 사용하는 한국인 칩이나, GWAS 연구 목적으로 사용되는 PRMA 칩 수백-백만개 마커 | ||
| he critical difference between Sanger sequencing and NGS is sequencing volume. While the Sanger method only sequences a single DNA fragment at a time, NGS is massively parallel, sequencing millions of fragments simultaneously per run. | |||||
| Sanger Sequencing | Targeted NGS | |
|---|---|---|
| Benefits |
- Fast, cost-effective sequencing for low numbers of targets (1–20 targets) - Familiar workflow |
- Higher sequencing depth enables higher sensitivity (down to 1%) - Higher discovery power - Higher mutation resolution† - More data produced with the same amount of input DNA‡ - Higher sample throughput |
| Challenges |
- Low sensitivity (limit of detection ~15–20%) - Low discovery power - Not as cost-effective for high numbers of targets (> 20 targets) - Low scalability due to increasing sample input requirements |
- Less cost-effective for sequencing low numbers of targets (1–20 targets) - Time-consuming for sequencing low numbers of targets (1–20 targets) |
- * Discovery power is the ability to identify novel variants.
- † Mutation resolution is the size of the mutation identified. NGS can identify large chromosomal rearrangements down to single nucleotide variants.
- ‡ 10 ng DNA will produce ~1 kb with Sanger sequencing or ~300 kb with targeted resequencing (250 bp amplicon length × 1536 amplicons with an AmpliSeq for Illumina workflow)
Human Genome Project
Genetic Testing
(et al. 2013, PMID 23588557) 2020 wallace
| included | excluded | description | Pros | cons | |
|---|---|---|---|---|---|
| sequencing of all ions of GBA1 | |||||
| screening for 5 to 10 specific variants | |||||
| screening for 2 to 4 specific variants |
Uncertain Spans
- Page 본문 최상단의 옛 entry “date 2012-11-01 p.*32/Argext*?” 줄의 “(alternatively p.Ter32ArgextTer? or p.*32/Rext?)” 괄호 안 표기는 photo 좌단에서 글자 일부가 잘려 시각 추정. 정확한 별칭 표기는 본 페이지에서 확정 불가.
- Genotyping Methods 표 ‘result’ 행 ‘TaqMan’ 열의 ‘일부적’은 사진에서 흐릿하여 시각 추정. ‘microarray / Sanger / NGS’ 열의 result 셀은 사진에서 거의 비어 있어 빈 셀로 보존했다.
- Genetic Testing 표의 ‘sequencing of all ions of GBA1’에서 ‘ions’는 ‘mutations’ 또는 다른 단어의 일부일 가능성이 있으나 사진 좌단에 글자가 일부 가려 시각 그대로 ‘ions’로 옮겼다.
- ‘NEW’ 노란 하이라이트는 본문 ‘NEW’ 라벨 자체가 강조되어 있으며, 별도 emoji-style 마커 없이 본문 굵게 표기로만 옮겼다.