Selection and optimization of STR for Shanghai Han population

doi:10.3969/j.issn.1673-8640.2016.09.012

Abstract

Abstract:

Objective To select common chromosome short tandem repeat（STR） for Shanghai Han population,and to optimize the site amplification conditions into a determination system. Quantitation fluorescence polymerase chain reaction（QF-PCR） will be used for the rapid prenatal diagnosis of fetal common chromosome aneuploidies. Methods Through the polymorphism analysis of 48 healthy Han population in Shanghai,STR heterozygosities on 13,18,21,X and Y chromosomes were evaluated. STR with high polymorphism was selected and optimized into a determination system,and the sensitivity and specificity were evaluated in the determination system by 36 samples [22 cases of amniotic fluid,9 cases of cord blood and 5 cases of chorionic villus samples（CVS）]. Chromosome karyotype analysis was performed simultaneously,and the effectiveness of the established method was evaluated. Results A total of 14 STR were selected in STR heterozygosity test,and they were D13S258（0.88）,D13S305（0.90）,D13S634（0.92）,D13S742（0.83）,D18S535（0.81）,D18S1002（0.69）,D18S386（0.75）,D18S391（0.77）,D21S1435（0.75）,D21S1412（0.94）,D21S1446（0.58）,D21S1414（0.85）,DXS7132（0.77） and DXY218（0.71）,together with sex chromosome of qualitative and quantitative specific STR of AMXY,SRY and TAF9B into optimizing an amplification system. The system was used to determine 36 samples of amniotic fluid,cord blood and CVS. There were 35 cases with abnormal chromosome numbers,including 15 cases of trisomy 21（Down's）,12 cases of trisomy 18（Edward）,4 cases of trisomy 13（Patau）,2 cases of 45,XO（Turner）,1 case of 47,XXY（Klinefelter） and 1 case of 47,XYY（Super-Man）. The remaining 1 case was 46,XX（healthy female）. The results of QF-PCR were as same as the results of chromosome karyotype analysis. Conclusions Selected 14 STR show high polymorphism in Shanghai Han population,and sex chromosome qualitative and quantitative specific STR constitute a QF-PCR determination system,which can accurately determine 13,18,21,X and Y chromosome aneuploidies. QF-PCR is a rapid,accurate,economic and efficient method for the rapid prenatal diagnosis of fetal common chromosome aneuploidies in Shanghai Han population.

Key words: Short tandem repeats, Heterozygosity, Prenatal diagnosis, Chromosome aneuploidies

CLC Number:

R446.1

ZHAO Huijia, GU Zhidong, CHENG Weiwei, TAO Jiong, GAO Jiaqi, HAN Xu. Selection and optimization of STR for Shanghai Han population[J]. Laboratory Medicine, 2016, 31(9): 787-791.

Figures/Tables 4

References 14

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序号	探针对名称	染色体	荧光标记	产物长度范围（bp）	引物结合的模板DNA序列1（5'~3'）	引物结合的模板DNA序列2（5'~3'）
1	TAF9B	X/3	蓝色	116~121	GCCTAGGTTCTAGTCCTAGCTCCATCA	ACCTACCCTGCCTACCTCACAGG
2	D13S742	13	蓝色	219~289	CCAGATAACTGGGCTAGGAATGGA	TGAATGCAAATTCTCTGGCCC
3	DXS7132	X	蓝色	299~359	ACCACTCCTGGTGCCAAACTCT	AGAATATGGGGAGCCGCTCATG
4	D21S1446	21	蓝色	379~429	TTTGGTCAATGGCAGATTGCATA	TAGCCTCGAGCAGGTCCTTTG
5	D18S391	18	绿色	149~181	CCCAGTTAGACTTCACTATTCCCATCT	TTCCTCAAGTCACATTGCCTGTG
6	AMXY	X/Y	绿色	189~199	GGCACCCTGGTTATATCAACTTCAG	CAGCTTCCCAGTTTAAGCTCTGATG
7	D13S258	13	绿色	209~285	GGAGGAGAGGGACTACCCAGACA	TTGGTTTATTCCCTCTCTCTGTCTTCC
8	D21S1414	21	绿色	379~425	TGGTCTGTTATGGGACTTTTCTCAGTC	TTTTTACTGGGTGCCAGACACTAATT
9	D13S305	13	绿色	439~509	ATGCAAGGAAATTTGTGGTTATAGAGC	ATTCGTAACGACAGGTCCTCAAACA
10	DXYS218	X/Y	黑色	119~155	GCGAAACTCCGTCTCAAAATAAATACA	CAGTTGGCACGCCTGACTTCTT
11	D21S1435	21	黑色	166~210	CCCATTCCCCTCTCCAATTGTT	TTGATGGCACTGAAATCTCTTGC
12	D21S1412	21	黑色	260~320	TGCTTCACATGTTTTCTTGACACAG	CAACTCACTGCAACCTCCGC
13	D18S1002	18	黑色	379~419	TTAGGGCATTGAGGCGTTTGAT	ATGTCTCCTGGCCTTTGCTCAG
14	SRY	Y	红色	129-~33	TTGCACTTCGCTGCAGAGTACC	TTTCTCTCTGTGCATGGCCTGT
15	D18S535	18	红色	151~201	TGTGACAAAAGCCACACCCATAA	TTATGGGTAACTCTTAGCCTGCCA
16	D13S634	13	红色	389~436	TCCATTGCCCTATCTTTAAGTTTGC	GGAAAGCCAGTAGTGTGGCAACAT
17	D18S386	18	红色	472~555	GCTGAGTCAGGAGAATCACTTGGAAC	GCATTAGGGTCTAAAATGTGCAATGT

序号	探针对名称	染色体	荧光标记	产物长度范围（bp）	引物结合的模板DNA序列1（5'~3'）	引物结合的模板DNA序列2（5'~3'）
1	TAF9B	X/3	蓝色	116~121	GCCTAGGTTCTAGTCCTAGCTCCATCA	ACCTACCCTGCCTACCTCACAGG
2	D13S742	13	蓝色	219~289	CCAGATAACTGGGCTAGGAATGGA	TGAATGCAAATTCTCTGGCCC
3	DXS7132	X	蓝色	299~359	ACCACTCCTGGTGCCAAACTCT	AGAATATGGGGAGCCGCTCATG
4	D21S1446	21	蓝色	379~429	TTTGGTCAATGGCAGATTGCATA	TAGCCTCGAGCAGGTCCTTTG
5	D18S391	18	绿色	149~181	CCCAGTTAGACTTCACTATTCCCATCT	TTCCTCAAGTCACATTGCCTGTG
6	AMXY	X/Y	绿色	189~199	GGCACCCTGGTTATATCAACTTCAG	CAGCTTCCCAGTTTAAGCTCTGATG
7	D13S258	13	绿色	209~285	GGAGGAGAGGGACTACCCAGACA	TTGGTTTATTCCCTCTCTCTGTCTTCC
8	D21S1414	21	绿色	379~425	TGGTCTGTTATGGGACTTTTCTCAGTC	TTTTTACTGGGTGCCAGACACTAATT
9	D13S305	13	绿色	439~509	ATGCAAGGAAATTTGTGGTTATAGAGC	ATTCGTAACGACAGGTCCTCAAACA
10	DXYS218	X/Y	黑色	119~155	GCGAAACTCCGTCTCAAAATAAATACA	CAGTTGGCACGCCTGACTTCTT
11	D21S1435	21	黑色	166~210	CCCATTCCCCTCTCCAATTGTT	TTGATGGCACTGAAATCTCTTGC
12	D21S1412	21	黑色	260~320	TGCTTCACATGTTTTCTTGACACAG	CAACTCACTGCAACCTCCGC
13	D18S1002	18	黑色	379~419	TTAGGGCATTGAGGCGTTTGAT	ATGTCTCCTGGCCTTTGCTCAG
14	SRY	Y	红色	129-~33	TTGCACTTCGCTGCAGAGTACC	TTTCTCTCTGTGCATGGCCTGT
15	D18S535	18	红色	151~201	TGTGACAAAAGCCACACCCATAA	TTATGGGTAACTCTTAGCCTGCCA
16	D13S634	13	红色	389~436	TCCATTGCCCTATCTTTAAGTTTGC	GGAAAGCCAGTAGTGTGGCAACAT
17	D18S386	18	红色	472~555	GCTGAGTCAGGAGAATCACTTGGAAC	GCATTAGGGTCTAAAATGTGCAATGT

染色体	STR位点	等位基因数	杂合度	染色体位置	染色体	STR位点	等位基因数	杂合度	染色体位置
Chr13	D13S628	7	0.67	13q31-q32	Chr21	D21S1437	8	0.48	21q21.1
	D13S742	6	0.83	13q12.12		D21S1446	8	0.58	21q22.3-ter
	D13S631	17	0.85	13q31-32		D21S1809	9	0.73	21q22.1
	D13S258	11	0.88	13q21		D21S1435	7	0.75	21q21
	D13S305	11	0.90	13q12.1-13q14.1		D21S1411	8	0.81	21q22.3
	D13S634	13	0.92	13q14.3		D21S1414	10	0.85	21q21
Chr18	D18S390	5	0.56	18q22.2		D21S1412	16	0.94	21q22.2
	D18S858	4	0.58	18q21.1	ChrX/Y	HPRT	5	0.60	Xq26.1
	D18S1002	5	0.69	18q11.2		DXS6803	7	0.67	Xq12-Xq21.33
	D18S386	16	0.75	18q22.1		SBMA	15	0.77	Xq11.2-Xq12
	D18S391	4	0.77	18pter-18p11.22		DXS6809	7	0.85	Xq
	D18S535	8	0.81	18q12.2		DXS8377	15	0.90	Xq28
	D18S499	9	0.83	18q21.32-q21.33		DXYS218	5	0.71	Xp22.32 Yp11.3（PAR1）
						X22	7	0.79	Xq28 Yq（PAR2）
						DXS7132	6	0.77	Xq12

染色体	STR位点	等位基因数	杂合度	染色体位置	染色体	STR位点	等位基因数	杂合度	染色体位置
Chr13	D13S628	7	0.67	13q31-q32	Chr21	D21S1437	8	0.48	21q21.1
	D13S742	6	0.83	13q12.12		D21S1446	8	0.58	21q22.3-ter
	D13S631	17	0.85	13q31-32		D21S1809	9	0.73	21q22.1
	D13S258	11	0.88	13q21		D21S1435	7	0.75	21q21
	D13S305	11	0.90	13q12.1-13q14.1		D21S1411	8	0.81	21q22.3
	D13S634	13	0.92	13q14.3		D21S1414	10	0.85	21q21
Chr18	D18S390	5	0.56	18q22.2		D21S1412	16	0.94	21q22.2
	D18S858	4	0.58	18q21.1	ChrX/Y	HPRT	5	0.60	Xq26.1
	D18S1002	5	0.69	18q11.2		DXS6803	7	0.67	Xq12-Xq21.33
	D18S386	16	0.75	18q22.1		SBMA	15	0.77	Xq11.2-Xq12
	D18S391	4	0.77	18pter-18p11.22		DXS6809	7	0.85	Xq
	D18S535	8	0.81	18q12.2		DXS8377	15	0.90	Xq28
	D18S499	9	0.83	18q21.32-q21.33		DXYS218	5	0.71	Xp22.32 Yp11.3（PAR1）
						X22	7	0.79	Xq28 Yq（PAR2）
						DXS7132	6	0.77	Xq12

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