SILK

Three major purpose of DNA QC

	Nucleic Acid Quantification	Nucleic Acid Purity (to see whether Contaminants such as RNA, proteins or chemicals)	Nucleic Acid Integrity (Size distribution) (to see whether the samples are fragmented or contaminated by other DNA or RNA products.)
Absorbance Method			Agarose Gel Electrophoresis	Capillary Electrophoresis
Fluorescence Method	NanoDrop™	UV spectrophotometry, qPCR		eg Femto pulse
	Thermo Scientific (Invitrogen) Qubit™ Fluorometer: Invitrogen Qubit 4 Fluorometer is designed for rapid and specific quantification of DNA and RNA.

Mutations

다른 방식 분류

		의미				Resulting Protein	Example
Germline cell mutation	Large scale m	Chromosome level에서	loss/gain of whole chromosome				Trisomy (21번 염색체 증가)
			Part of chromosome	translocation
		inversion
		insertion
		duplication (amplification),, 이게 copy number variation이겠다 (CMT1A 이렇게 불리더라)
		amplification
		deletion
	Small scale m	Nucleotide level에서 (ie base)	Substitution m (Point m)	SNP위치가 exon	Silent m	code for the same aa	Same functional protein	하나의 단백질로 전사되는 3개의 염기 TCA(Serine) 중 세 번째 염기인 A가 C로 변이가 일어나도(즉, TCC) 단백질은 동일하게 세린(Serine)으로 전이
					Missense m	DNA 염기 하나가 다른 종류의 염기로 바뀜, & code for a different aa	nonfunctional	Sicle cell anemia
					Nonsense m	DNA 염기 하나가 다른 종류의 염기로 바뀜 & a codon is changed to a stop codon	Truncated protein	DMD
				SNP위치가 intron (이게 최빈발)
				SNP위치가 promoter
			Frameshift	Insertions Deletions	원래 Codon (=three nucleotide)단위로 읽으니, 완전히 다른 생산물이 나오겠다.
			Tandem repeat (같은 nucleotide가 반복)
		Copy number variation		Eg. deletion and duplication of exon (?)
	Splice site mutation		definition	a genetic mutation that inserts, deletes or changes a number of nucleotides in the specific site at which splicing takes place during the processing of precursor messenger RNA into mature messenger RNA. The mutation can be an insertion, deletion, frameshift, etc Mutations in these sequences may lead to retention of large segments of intronic DNA by the mRNA, or to entire exons being spliced out of the mRNA. These changes could result in production of a nonfunctional protein.[2] The splicing mutation may occur in both introns and exons A genetic alteration in the DNA sequence that occurs at the boundary of an exon and an intron (splice site). This change can disrupt RNA splicing resulting in the loss of exons or the inclusion of introns and an altered protein-coding sequence. Also called splice-site variant.
	pitt		Nomenclature	- 이것의 특정 nomenclature는 없이, 결과에 따라 달라짐.
Somatic cell mutation			These mutations occur from damage to genes in an individual cell during a person's life. Somatic mutations or acquired mutations are not found in every cell in the body and they are not passed from parent to child. Oncology (BRAF, K-RAS, EGFR mutation)

compound heterozygous: when both alleles of a gene harbor mutations, but the mutations are different (양 allele 이 다 mutation 이므로, homozygous 만큼 심하여, homozygous mutation 류로 간주됨 (이게 GD 를 일으키므로, (Gan-Or et al. 2018, PMID 29884970)

SNP Database

https://www.ncbi.nlm.nih.gov/snp/rs55961220

	dbSNP https://www.ncbi.nlm.nih.gov/snp/rs5596122 0	VARVIEW https://www.ncbi.nlm.nih.gov/variation/view/?q=rs55777503	ClinVar https://www.ncbi.nlm.nih.gov/clinvar/	VEP (Ensembl) Variant Effect Predictor https://asia.ensembl.org/info/docs/tools/vep/index.html	He lix	OMIM	UCSC Genome Browser https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&po sition=chr6%3A162265237-162265306&hgsid=1102471205_QwGYKLNNGsgZ8QyfBmqA01b5z6r	VARSO ME https://varsome.com/gene/prkn	PDGENE http://www.pdgene.org/view?poly=rs3734464	Parkinson's Disease Sequencing Browser https://pdgenetics.shinyapps.io/VariantBrowser/
-	Pathogenic, variation type 등 고를 수 있음 Prkn의 pathogenic : 20 items (all with rs)	Pathogenic, variation type 등 고를 수 있음.							{Kim, 2021 #2378} Looks easy and good
-				predicted LoF (VEP LOFTEE)	deleterious missense	(이상문) 이것도 Pathogenicity 판단한다고..		Pthogenicity를 ACMG에 따라 확실히 verdict 해줌.
-									https://pdgenetics.shinyapps.io/VariantBrowser/
VARIAnt type	Variant ID	VARIAnt type	variation ID
SNV	rs
		Copy number variation
del	rs55777503	Copy number variation	nsv3877040
	dbSNP : rs572345942		Accession: VCV000356004.1				Find base info etc using Position info: 위에 coordinate 를 입력 into chr6:161,807,855 (base 단위로 볼 수 있음.)
delins	rs (rs 없음)

Uncertain Spans

• ‘Mutations’ 표의 좌측 두 컬럼(‘Germline cell mutation’ / ‘Large scale m’ / ‘Chromosome level에서’ 등)에 보이는 주석 한국어 메모 일부는 사진에서 약간 흐릿하나 시각 판독 가능한 수준에서 옮겼다. ‘pitt’ (Nomenclature 행 좌측 라벨)의 정확한 의미·약자는 본 페이지에서 확정 불가.
• ‘Splice site mutation’ 정의 셀은 colspan으로 묶었으나 원본 Word 셀 분할 경계는 사진에서 모호하다 — 원문 cell granularity는 KB 재구성 단계에서 재검증 필요.
• SNP Database 표의 Helix 컬럼은 머리행이 ‘He / lix’로 줄바꿈되어 있어 한 단어 ‘Helix’로 합쳐 옮겼다. UCSC Genome Browser 링크는 사진에서 매우 작아 다중 토큰 일부(‘hgsid’ 뒷부분 등)는 시각 추정.
• SNP Database 표의 ‘delins / rs (rs 없음)’ 행 의미는 본문에 명확한 설명이 없어 위치 매핑만 보존하였다.