Patent Grant
11345948
The present application is a national phase entry under 35 U.S.C. § 371 of International Application No. PCT/CN2016/070696, filed on Jan. 19, 2016, the content of which is hereby incorporated by reference in its entity.
The present application contains a Sequence Listing which has been submitted via EFSWeb and is hereby incorporated by reference in its entirety. The ASCII copy, created on Jul. 9, 2018, is named 00242_0001sequencelisting.txt, and is 156 kilobytes in size.
The present disclosure relates to molecular diagnosis and particularly relates to a method for detecting chromosomal Robertsonian translocation, which is capable of detecting normal and translocation carrying embryo and fetus, of which the parents have pedigree of Robertsonian translocation.
Robertsonian translocation (ROB) is named according to the American biologist William Rees Brebner Robertson who for the first time found the translocation pattern and is a chromosomal translocation mainly occurring in 5 acrocentric chromosomes (Chromosome 13, Chromosome 14, Chromosome 15, Chromosome 21 and Chromosome 22) (Robertson WRB. Chromosome studies. I. Taxonomic relationships shown in the chromosomes of Tettigidae and Acrididae. V-shaped chromosomes and their significance in Acrididae, Locustidae and Gryllidae: chromosome and variation. J Morph 1916, 27: 179-331). When two acrocentric chromosome break at centromere or a location in proximity to centromere, their long arms bind at centromere forming a derived chromosome composed of long arms, which is also known as centromere fusion, one of chromosomal balanced translocations. Two short arms form a small chromosome, which always loses in a second division. Robertsonian translocation is a common chromosomal abnormal structure, of which the newborn occurrence rate is 1.23/1000 (Nielsen J, Wohlert M. Chromosome abnormalities found among 34910 newborn children: results from 13-year incidence study in Arhus, Denmark. Hum Genet. 1991, 87: 81-83). As the short arm of chromosome mainly comprises random repeated DNA and ribosome RNA genes, which are present in all of the five chromosome, there is loss of short arm of chromosome in Robertsonian translocation, it does not results in pathogenic phenotype. Although the phenotype is normal, during the Pt meiosis of carrier's germ cell, the translocation chromosome and two corresponding normal chromosome will match to form trivalent chromosome and such a structure will result in three division patterns, i.e. alternate, neighborhood and uncommon 3:0 division patterns, of which only the alternate pattern will lead to normal or balanced gametes and others will lead to unbalanced gametes. The dominating unbalanced gametes will lead to difficulty in pregnancy or recurrent abortion in pregnancy, and even lead to birth of children with congenital defect like 13-Patau syndrome with abnormal chromosome copy number in translocation carrier. Now more and more Robertsonian translocation carriers seek for test-tube baby technology for preimplantation genetic diagnosis.
The test-tube baby is a technology that ovum and sperm are taken to put in a special culture liquid for culture, fertilization, and the oosperm develops into an embryo in a thermostat incubator, which is then transplanted into parent uterus where it develops into a fetus finally.
A key of successful prevention lies in selecting health embryo for transplant. Preimplantation genetic screen refers to detection of chromosome number and abnormal structure before implantation and nidation of an embryo, selection for an embryo with normal chromosome for implantation into uterus, so as to give normal progeny. The current preimplantation genetic diagnosis for Robertsonian translocation comprises SNP chip and fluorescence in situ hybridization (FISH). The SNP chip is the most commonly used detection technology, which however can only detect embryo chromosome copy number change but cannot differentiate normal embryo from translocation carrying translocation in Robertsonian translocation. FISH uses specific nucleic acid probe labeled with fluorescence to hybrid with corresponding target DNA molecule in cells, and fluorescence signal is observed under fluorescence microscope to determine the location of DNA molecule bound with fluorescence probe in chromosome. Nevertheless, FISH as a method for examine single nucleus has some defect as 7% false negative rate (Colls P, Escudero T, Cekleniak N, Sadowy S, Cohen J, Munné S. Increased efficiency of preimplantation genetic diagnosis for infertility using “no result rescue”. Fertil Steril. 2007, 88(1): 53-61).
Spontaneous abortion is a common disease in gynaecology and obstetrics, of which the occurrence rate account for 10%-15% of all the pregnancy. The occurrence rate is determined by many factors, like embryo factor, placenta factor, parent factor, environmental factor or the like, wherein abnormal embryo chromosome is the main cause of abortion.
Chromosomal examination on abortion tissue for the causes of embryo developmental arrest, abortion provides theoretical basis for clinical counsel and guideline for subsequent pregnancy. Now FISH technology is for use in performing common abnormal chromosome on missed abortion villus and tissues at different locations of a fetus. FISH as a targeted detecting technology has limited commercial probes and was limited by the type, amount and high cost of the probes. It cannot detect a large number of abnormal genes or chromosome. Additionally, due to the limit of FISH, it cannot be used to detect chromosomal abnormal structure, leading to missed diagnosis of some patients with chromosomal abnormal structure (L I, Yangyang, Zhang Qin, Current study of analysis of spontaneous abortion villus chromosome karyotype, Journal of Obstetrics and Gynaecology, 2012, 28: 431-433).
In a summary, it is desired to develop a novel method to detect Robertsonian translocation of embryo and abortion tissue in test-tube baby technology.
Provided is a method for detecting chromosomal Robertsonian translocation based on high-throughput sequencing technology so as to screen fully normal and translocation carrying embryo, fetus or abortion tissue.
In the first aspect, provided is a method for detecting chromosomal Robertsonian translocation, comprising the steps of:
(1) obtaining DNA samples from both of the parents and the progeny;
(2) screening hypermutational SNP site from a location in proximity to the centromere of acrocentric chromosome as a marker;
(3) detecting chromosome copy number of the progeny DNA sample;
(4) determining genotypes of the target sites of both of the parents and the progeny according to the SNP site screened in step (2);
(5) analyzing haplotypes of both of the parents and the progeny based on the genotypes and pedigree relations of both of the parents and the progeny;
(6) analyzing the chromosomal Robertsonian translocation of the progeny according to the detecting result of chromosome copy number of the progeny, the karyotypes of both of the parents carrying chromosomal Robertsonian translocation and the haplotypes of both of the parents and the progeny.
Preferably, the method is useful for detecting human chromosomal translocation, particularly the translocation between any two chromosomes of Chromosome 13, Chromosome 14, Chromosome 15, Chromosome 21 and Chromosome 22.
In a specific embodiment, the parental DNA sample is the parental genomic DNA extracted from peripheral blood sample; the progeny DNA sample is selected from the group consisting of trophoblast cell whole genomic amplified products of embryo or fetus or genomic DNA extracted from abortion tissue, preferably blastocyst trophoblast cell whole genomic amplified product of embryo cultured in vitro.
In the above step (2), the screening criteria for SNP site are:
a. the site is within 10 Mb location in proximity to the centromere;
b. the site is collected in 1000 Genomes database or dbSNP database, preferably SNP of which the Minimum Allele Frequency (MAF) in target population is above 0.2;
c. the sequence in proximity to the SNP site is not homologous in human genome.
In a particular embodiment, the SNP sites comprise at least one SNP site, preferably at least 10 SNP sites, more preferably at least 50 SNP sites from every chromosome with translocation.
Preferably, the SNP site is selected from the group consisting of the following SNP sites or any combination thereof: chr13:19602195, chr13:19625370, chr13:19646283, chr13:19692745, chr13:19713634, chr13:19722801, chr13:19732341, chr13:19784913, chr13:19843135, chr13:19877547, chr13:19883672, chr13:19896927, chr13:19917509, chr13:20494558, chr13:20709214, chr13:20747500, chr13:20784332, chr13:20825315, chr13:20864572, chr13:20881859, chr13:20908501, chr13:20938952, chr13:20951425, chr13:20992333, chr13:21012562, chr13:21066214, chr13:21092894, chr13:21112935, chr13:21527671, chr13:21553971, chr13:21575458, chr13:21607760, chr13:21636136, chr13:21655335, chr13:21683681, chr13:21801501, chr13:22197910, chr13:22249975, chr13:22270788, chr13:22340074, chr13:22396664, chr13:22417688, chr13:22473749, chr13:22504691, chr13:22515844, chr13:22523279, chr13:22538311, chr13:22561684, chr13:22640820, chr13:22751654, chr13:22768476, chr13:22780737, chr13:22799808, chr13:22819627, chr13:22835073, chr13:22892864, chr13:22980146, chr14:19472367, chr14:20326905, chr14:20349694, chr14:20383719, chr14:20420387, chr14:20517369, chr14:20527044, chr14:20565487, chr14:20643775, chr14:20670979, chr14:20731036, chr14:20820537, chr14:20905141, chr14:20918598, chr14:21008574, chr14:21048774, chr14:21091127, chr14:21156472, chr14:21195967, chr14:21237137, chr14:21263166, chr14:21313819, chr14:21325985, chr14:21388266, chr14:21452591, chr14:21519915, chr14:21580671, chr14:21625262, chr14:21789092, chr14:21981923, chr14:22053817, chr14:22090208, chr14:22138437, chr14:22210067, chr14:22244363, chr14:22263821, chr14:22312275, chr14:22324460, chr14:22351977, chr14:22361282, chr14:22375208, chr14:22393124, chr14:22428984, chr14:22452496, chr14:22489611, chr14:22518909, chr14:22526966, chr14:22563283, chr14:22611651, chr14:22626948, chr14:22657897, chr14:22702039, chr14:22731529, chr14:22734948, chr14:22741160, chr14:22772663, chr14:22861948, chr14:22972955, chr15:20022190, chr15:20049922, chr15:20189367, chr15:20191854, chr15:20192138, chr15:20454253, chr15:20470948, chr15:20564500, chr15:20569241, chr15:20586537, chr15:20586966, chr15:20590656, chr15:20616721, chr15:20626721, chr15:20646773, chr15:20848359, chr15:20849625, chr15:20852181, chr15:20862156, chr15:20863958, chr15:21905797, chr15:21928397, chr15:21938184, chr15:21940649, chr15:22013203, chr15:22299435, chr15:22302182, chr15:22376163, chr15:22427155, chr15:22441959, chr15:22476195, chr15:22520388, chr15:22539952, chr15:22780065, chr15:22798800, chr15:22833272, chr15:22854479, chr15:22869870, chr15:22893990, chr15:22905599, chr15:22916637, chr15:22923869, chr15:22940961, chr15:22971662, chr15:23000363, chr15:23010627, chr15:23020535, chr15:23044004, chr15:23053813, chr15:23064687, chr15:23721906, chr15:23730971, chr15:23746510, chr15:23767135, chr15:23781336, chr15:23793989, chr15:23816231, chr15:23893430, chr15:23929209, chr15:24006330, chr15:24055535, chr15:24129894, chr15:24166516, chr15:24196094, chr15:24236177, chr15:24278723, chr15:24319610, chr15:24350583, chr15:24471640, chr15:24824114, chr15:24870875, chr15:24913763, chr15:24943341, chr15:24974072, chr21:14640496, chr21:14643423, chr21:14695894, chr21:14756515, chr21:14818516, chr21:14890028, chr21:15012159, chr21:15026905, chr21:15170049, chr21:15280687, chr21:15300595, chr21:15445542, chr21:15479041, chr21:15501432, chr21:15548748, chr21:15566056, chr21:15588845, chr21:15625530, chr21:15654618, chr21:15681452, chr21:15720558, chr21:15763305, chr21:15842397, chr21:15884516, chr21:15916232, chr21:15942816, chr21:15984234, chr21:16027704, chr21:16063848, chr21:16122140, chr21:16160041, chr21:16193235, chr21:16238898, chr21:16315932, chr21: 16353639, chr21:16384555, chr21: 16448591, chr21: 16578538, chr21: 16645724, chr21:16717265, chr21:16833315, chr21:16881542, chr21:17000938, chr21:17054831, chr21:17140290, chr21:17203891, chr21:17295288, chr21:17340912, chr21:17536247, chr21: 17640426, chr21: 17673255, chr21: 17713264, chr21: 17748703, chr21: 17781159, chr21: 17823782, chr21: 18003355, chr21: 18046650, chr21: 18114449, chr21:18151760, chr21: 18182817, chr21:18250262, chr21: 18337678, chr21: 18385770, chr21: 18420873, chr21: 18457287, chr21:18586049, chr21: 18650837, chr21: 18740886, chr21: 18858018, chr21:18936951, chr21:19002939, chr21:19064396, chr21:19139888, chr21:19254923, chr21: 19316600, chr22:16415691, chr22: 16554800, chr22: 16848067, chr22: 16850056, chr22: 16850858, chr22:16851557, chr22: 16852464, chr22: 16852792, chr22: 16853453, chr22: 16854397, chr22:16855647, chr22: 16856500, chr22: 16857432, chr22: 16858287, chr22: 16860547, chr22:16861742, chr22: 16867995, chr22: 17031697, chr22: 17271213, chr22:17293257, chr22:17409957, chr22:17442318, chr22:17469090, chr22:17525677, chr22: 17563259, chr22: 17587785, chr22: 17619511, chr22: 17656792, chr22:17682387, chr22: 17715164, chr22: 17739757, chr22: 17761489, chr22: 17785311, chr22: 17805528, chr22: 17841251, chr22: 17883346, chr22: 17916190, chr22: 17939998, chr22: 17981144, chr22: 18012297, chr22:18054406, chr22: 18212058, chr22: 18276198, chr22: 18354015, chr22: 18395978, chr22:18466951, chr22: 18531582, chr22: 18581715, chr22: 18628321, chr22:18894617, chr22:18966077, chr22:19004846, chr22:19025459, chr22:19098323, chr22: 19142652, chr22:19236590, chr22: 19362714, chr22: 19431588, chr22: 19536367, chr22: 19643965, chr22:19716983, chr22: 19759532, chr22: 19808057, chr22: 19859087, chr22:19909387, chr22:19972494, chr22:20016622, chr22:20051573, chr22:20081918, chr22:20135421, chr22:20175034, chr22:20216874, chr22:20278637, chr22:20745699, chr22:20787955, chr22:20855585, chr22:20881195, chr22:20924097, chr22:20983921, chr22:21028224. Most preferably, the SNP sites comprise all the above SNP sites from every chromosome with translocation.
In a particular embodiment, the process for detecting the chromosome copy number in above step (3) and step (4) is selected independently from the group consisting of sequencing process and chip process. The sequencing process is a high-throughput sequencing process, preferably Ion Torrent PGM or Illumina Miseq; the chip process is human whole genomic SNP chip, preferably Illumina whole genomic SNP chip.
Preferably, in the detecting method according to the invention, one of the parents has normal karyotype, the other carries Robertsonian translocation; the progeny comprises a subject that is Robertsonian translocation chromosome trisomic or monosomic.
Specifically, the determining criteria in step (6) are:
a. if a progeny is chromosome m trisomic, haplotype B in chromosome n from parental Robertsonian translocation carrier is translocation chromosome haplotype, and accordingly another haplotype b in chromosome n from parental Robertsonian translocation carrier is normal chromosome haplotype; and further by observing haplotype of other progeny, chromosome m haplotype A from parental Robertsonian translocation carrier linked with chromosome n haplotype B is translocation chromosome haplotype, and accordingly, another haplotype a in chromosome m from parental Robertsonian translocation carrier is normal chromosome haplotype; thereby it can be determined that the progeny carrying chromosome m haplotype A and chromosome n haplotype B is translocation carrier, and the progeny carrying chromosome m haplotype a and chromosome n haplotype b is normal karyotype;
b. if a progeny is chromosome m monosomic, haplotype B in chromosome n from parental Robertsonian translocation carrier is normal chromosome haplotype, and accordingly another haplotype b in chromosome n from parental Robertsonian translocation carrier is translocation chromosome haplotype; and further by observing haplotype of other progeny, chromosome m haplotype a from parental Robertsonian translocation carrier linked with chromosome n haplotype b is translocation chromosome haplotype, and accordingly another haplotype A in chromosome m from parental Robertsonian translocation carrier is normal chromosome haplotype; thereby it can be determined that the progeny carrying chromosome m haplotype A and chromosome n haplotype B is normal karyotype, and the progeny carrying chromosome m haplotype a and chromosome n haplotype b is translocation carrier;
wherein chromosome m and chromosome n are two chromosomes with Robertsonian translocation in the genome of parental Robertsonian translocation carrier, A and a are haplotypes from parental Robertsonian translocation carrier chromosome m, and B and b are haplotype from parental Robertsonian translocation carrier chromosome n.
Taking chromosomal translocation in Chromosome 13 and Chromosome 14 as an example,
According to the above table, if Chromosome 13 is triploid or haploid, it can be inferred that B type in Robertsonian translocation carrier Chromosome 14 is translocation chromosome haplotype, b type is normal chromosome haplotype; according to other embryo carrying B type or b type, it can be further inferred that A type in Chromosome 13 is translocation chromosome haplotype, a type is normal chromosome haplotype;
if Chromosome 14 is triploid or haploid, it can be inferred that A type in Robertsonian translocation carrier Chromosome 13 is translocation chromosome haplotype, a type is normal chromosome haplotype; according to other embryo carrying A type or a type, it can be further inferred that B in Chromosome 14 is translocation chromosome haplotype, b is normal chromosome haplotype.
Therefore, carrier of Chromosome 13 a type and Chromosome 14 b type is normal embryo, and carrier of Chromosome 13 A type and Chromosome 14 B type is translocation carrier embryo.
The method according to the invention is particularly useful for preimplantation genetic diagnosis.
In the second aspect, provided is a primer composition for detecting chromosomal Robertsonian translocation, the primer composition is capable of amplifying the sequence of hypermutational SNP site in proximity to centromere of acrocentric chromosome. Preferably, the primer composition is for use in detecting human chromosomal Robertsonian translocation, particularly a translocation between any two of Chromosome 13, Chromosome 14, Chromosome 15, Chromosome 21 and Chromosome 22.
The screening criteria for SNP site are:
a. the site is within 10Mb location in proximity to the centromere;
b. the site is collected in 1000 Genomes database or dbSNP database, preferably SNP of which the Minimum Allele Frequency (MAF) in target population is above 0.2;
c. the sequence in proximity to the SNP site is not homologous in human genome.
In a specific embodiment, the SNP sites comprise at least one SNP site, preferably at least 10 SNP sites, more preferably at least 50 SNP sites from every chromosome with translocation.
Preferably, the SNP site is selected from the group consisting of the following SNP sites or any combination thereof: chr13:19602195, chr13:19625370, chr13:19646283, chr13:19692745, chr13:19713634, chr13:19722801, chr13:19732341, chr13:19784913, chr13:19843135, chr13:19877547, chr13:19883672, chr13:19896927, chr13:19917509, chr13:20494558, chr13:20709214, chr13:20747500, chr13:20784332, chr13:20825315, chr13:20864572, chr13:20881859, chr13:20908501, chr13:20938952, chr13:20951425, chr13:20992333, chr13:21012562, chr13:21066214, chr13:21092894, chr13:21112935, chr13:21527671, chr13:21553971, chr13:21575458, chr13:21607760, chr13:21636136, chr13:21655335, chr13:21683681, chr13:21801501, chr13:22197910, chr13:22249975, chr13:22270788, chr13:22340074, chr13:22396664, chr13:22417688, chr13:22473749, chr13:22504691, chr13:22515844, chr13:22523279, chr13:22538311, chr13:22561684, chr13:22640820, chr13:22751654, chr13:22768476, chr13:22780737, chr13:22799808, chr13:22819627, chr13:22835073, chr13:22892864, chr13:22980146, chr14: 19472367, chr14:20326905, chr14:20349694, chr14:20383719, chr14:20420387, chr14:20517369, chr14:20527044, chr14:20565487, chr14:20643775, chr14:20670979, chr14:20731036, chr14:20820537, chr14:20905141, chr14:20918598, chr14:21008574, chr14:21048774, chr14:21091127, chr14:21156472, chr14:21195967, chr14:21237137, chr14:21263166, chr14:21313819, chr14:21325985, chr14:21388266, chr14:21452591, chr14:21519915, chr14:21580671, chr14:21625262, chr14:21789092, chr14:21981923, chr14:22053817, chr14:22090208, chr14:22138437, chr14:22210067, chr14:22244363, chr14:22263821, chr14:22312275, chr14:22324460, chr14:22351977, chr14:22361282, chr14:22375208, chr14:22393124, chr14:22428984, chr14:22452496, chr14:22489611, chr14:22518909, chr14:22526966, chr14:22563283, chr14:22611651, chr14:22626948, chr14:22657897, chr14:22702039, chr14:22731529, chr14:22734948, chr14:22741160, chr14:22772663, chr14:22861948, chr14:22972955, chr15:20022190, chr15:20049922, chr15:20189367, chr15:20191854, chr15:20192138, chr15:20454253, chr15:20470948, chr15:20564500, chr15:20569241, chrl 5:20586537, chr15:20586966, chrl 5:20590656, chr15:20616721, chr15:20626721, chrl 5:20646773, chr15:20848359, chrl 5:20849625, chr15:20852181, chr15:20862156, chr15:20863958, chr15:21905797, chr15:21928397, chr15:21938184, chr15:21940649, chr15:22013203, chr15:22299435, chr15:22302182, chr15:22376163, chr15:22427155, chr15:22441959, chr15:22476195, chr15:22520388, chr15:22539952, chr15:22780065, chr15:22798800, chr15:22833272, chr15:22854479, chr15:22869870, chr15:22893990, chr15:22905599, chr15:22916637, chr15:22923869, chr15:22940961, chr15:22971662, chr15:23000363, chr15:23010627, chr15:23020535, chr15:23044004, chr15:23053813, chr15:23064687, chr15:23721906, chr15:23730971, chr15:23746510, chr15:23767135, chr15:23781336, chr15:23793989, chr15:23816231, chr15:23893430, chr15:23929209, chr15:24006330, chr15:24055535, chr15:24129894, chr15:24166516, chr15:24196094, chr15:24236177, chr15:24278723, chr15:24319610, chr15:24350583, chr15:24471640, chr15:24824114, chr15:24870875, chr15:24913763, chr15:24943341, chr15:24974072, chr21:14640496, chr21:14643423, chr21:14695894, chr21:14756515, chr21:14818516, chr21:14890028, chr21:15012159, chr21:15026905, chr21:15170049, chr21:15280687, chr21:15300595, chr21:15445542, chr21:15479041, chr21:15501432, chr21:15548748, chr21:15566056, chr21:15588845, chr21:15625530, chr21:15654618, chr21:15681452, chr21:15720558, chr21:15763305, chr21:15842397, chr21:15884516, chr21:15916232, chr21:15942816, chr21:15984234, chr21:16027704, chr21:16063848, chr21:16122140, chr21:16160041, chr21:16193235, chr21:16238898, chr21:16315932, chr21:16353639, chr21: 16384555, chr21:16448591, chr21:16578538, chr21:16645724, chr21:16717265, chr21:16833315, chr21:16881542, chr21:17000938, chr21:17054831, chr21:17140290, chr21:17203891, chr21:17295288, chr21:17340912, chr21:17536247, chr21:17640426, chr21:17673255, chr21:17713264, chr21:17748703, chr21:17781159, chr21:17823782, chr21:18003355, chr21:18046650, chr21:18114449, chr21:18151760, chr21:18182817, chr21:18250262, chr21:18337678, chr21:18385770, chr21:18420873, chr21:18457287, chr21:18586049, chr21:18650837, chr21:18740886, chr21:18858018, chr21:18936951, chr21:19002939, chr21:19064396, chr21:19139888, chr21:19254923, chr21:19316600, chr22:16415691, chr22:16554800, chr22:16848067, chr22:16850056, chr22: 16850858, chr22:16851557, chr22: 16852464, chr22: 16852792, chr22: 16853453, chr22: 16854397, chr22:16855647, chr22: 16856500, chr22: 16857432, chr22: 16858287, chr22: 16860547, chr22:16861742, chr22: 16867995, chr22: 17031697, chr22: 17271213, chr22: 17293257, chr22: 17409957, chr22: 17442318, chr22: 17469090, chr22: 17525677, chr22: 17563259, chr22: 17587785, chr22: 17619511, chr22: 17656792, chr22:17682387, chr22: 17715164, chr22: 17739757, chr22: 17761489, chr22: 17785311, chr22:17805528, chr22: 17841251, chr22: 17883346, chr22: 17916190, chr22: 17939998, chr22: 17981144, chr22: 18012297, chr22: 18054406, chr22: 18212058, chr22: 18276198, chr22: 18354015, chr22:18395978, chr22:18466951, chr22:18531582, chr22:18581715, chr22:18628321, chr22: 18894617, chr22: 18966077, chr22: 19004846, chr22: 19025459, chr22: 19098323, chr22: 19142652, chr22:19236590, chr22: 19362714, chr22: 19431588, chr22: 19536367, chr22: 19643965, chr22:19716983, chr22: 19759532, chr22: 19808057, chr22: 19859087, chr22: 19909387, chr22: 19972494, chr22:20016622, chr22:20051573, chr22:20081918, chr22:20135421, chr22:20175034, chr22:20216874, chr22:20278637, chr22:20745699, chr22:20787955, chr22:20855585, chr22:20881195, chr22:20924097, chr22:20983921, chr22:21028224. Most preferably, the SNP sites comprise all the above SNP sites from every chromosome with translocation
In a particularly preferable embodiment, the primer composition is selected from the group consisting of the following primer pair composed of the following forward primer and reverse primer, or any combination thereof:
(1) the primer for amplifying the SNP site in Chromosome 13, which is selected from the group consisting of following primer pairs: forward primer sequence SEQ ID NO:2n-1, reverse primer sequence SEQ ID NO:2n, n is a natural number selected from 1-57;
(2) the primer for amplifying the SNP site in Chromosome 14, which is selected from the group consisting of following primer pairs: forward primer sequence SEQ ID NO:2n-1, reverse primer sequence SEQ ID NO:2n; wherein n is a natural number selected from 58-115;
(3) the primer for amplifying the SNP site in Chromosome 15, which is selected from the group consisting of following primer pairs: forward primer sequence SEQ ID NO:2n-1, reverse primer sequence SEQ ID NO:2n; wherein n is a natural number selected from 116-189;
(4) the primer for amplifying the SNP site in Chromosome 21, which is selected from the group consisting of following primer pairs: forward primer sequence SEQ ID NO:2n-1, reverse primer sequence SEQ ID NO:2n; wherein n is a natural number selected from 190-264;
(5) the primer for amplifying the SNP site in Chromosome 22, which is selected from the group consisting of following primer pairs: forward primer sequence SEQ ID NO:2n-1, reverse primer sequence SEQ ID NO:2n wherein n is a natural number selected from 265-344.
Preferably, the primer composition comprises at least one pair of primers, preferably at least 10 pairs of primers, more preferably at least 50 pairs of primers for amplifying SNP site in every chromosome with translocation; and most preferably comprises all above primer pairs for amplifying SNP site in every chromosome with translocation.
Provided is also use of the primer composition according to the invention for the manufacture of a diagnostic reagent or kit for detecting chromosomal Robertsonian translocation.
The advantages of the invention are summarized as follows.
Applicability: The invention is capable of solving the detecting issue in embryo, fetus or abortion tissue Robertsonian translocation carrier, which is not possible for conventional methods.
Simplicity and Convenience: In the present invention, analysis of chromosomal translocation of various cells are based on cell chromosome copy number and haplotype without observation of the cells, thereby enable quick differentiation of normal and translocation carrying embryo.
Universality: Poly SNP is used in the present invention for analysis, which can be used in preimplantation genetic diagnosis, fetus diagnosis or abortion tissue diagnosis of different spouses.
High throughput: Based on high-throughput sequencing technology, the invention can be used to analyze chromosomal translocation and by different sequencing tags on each sample, a large number of samples can be analyzed at the same time.
Low cost: The detecting cost of chromosomal translocation of the invention is decreasing with the development of sequencing technology and decrease of sequencing cost.
High sensitivity: The invention can be used on the analysis for 3-5 cells. Accordingly, in addition to abortion tissue, trophoblast cell from cervix, the invention is particularly useful for preimplantation genetic diagnosis in test-tube baby technology.
Specificity: Hypermutational sites with Minimum Allele Frequency >0.2 of CHB (northern Han Chinese) and CHS (southern Han Chinese) within 10 Mb range in proximity to centromere location in chromosome in 1000 Genomes data are selected, wherein polymorphic sites with GC content >70% in polynucleotide (polyN) and upstream and downstream 50 bp sequences are excluded, and SNP mutant site which is uniquely aligned in human genome is selected as target location. Primers are designed by logging in https://www.ampliseq.com/ for submitting target site and location. These primers are highly specific.
Accuracy: According to change of translocation chromosome copy number and the sample carrying corresponding chromosome, the each derived chromosome haplotype in chromosome with translocation can be speculated, and higher accuracy can be achieved with mutual authentication.
In context of the invention, reads refers to sequence fragments obtained in sequencing.
In context of the invention, single nucleotide polymorphism (SNP) refers to DNA sequence polymorphism resulted from single nucleotide variation at genomic level.
In context of the invention, haplotype refers to a combination of a group of single nucleotide polymorphism in a specific location of a chromosome which is associated with each other and are intended to inherit to progeny entirely. It is also known as haploid or haplotype.
In context of the invention, embryo genomic DNA is obtained by enriching genomic DNA in cells with whole genomic amplifying process, when an embryo develops to blastula stage where 3-5 periphery trophoblast cell are taken.
In context of the invention, enrichment of DNA molecule in target location is performed with multiplex PCR amplification. The specific principle and procedures can be found in the manufacture's instruction, where the DNA molecule is enriched into fragments with certain lengths and relatively concentrated. In a specific embodiment according to the invention, DNA fragments have the lengths of 125-275 bp.
In the present invention, according to hypermutational SNP sites in proximity to acrocentric location of human Chromosome 13, Chromosome 14, Chromosome 15, Chromosome 21 and Chromosome 22, 57, 58, 74, 75 and 80 pairs of sequence specific primers are designed respectively (primer sequences and relevant SNP site information can be found in Table 1-5). These primers are characterized in that (1) unique in target chromosome; (2) have the same annealing temperature.
In the present invention, SNP site is indicated with the chromosome where the site is located and the location at the chromosome (hg19 reference genome sequence as standard), for example, chr13:19602195 indicates that the SNP site is located at 19602195 nucleotide in Chromosome 13, hg19 reference genome sequence.
In the present invention, the sequencing process used may be high-throughput sequencing technology. The lengths of DNA fragments are 125-275 bp. In a specific embodiment according to the invention, the sequencing platform is Ion Torrent PGM and DNA sequence molecules with DNA lengths of 125-275 bp are obtained.
In the present invention, the sequencing depth may be 3003000×, i.e. each specific PCR amplified product is sequenced for 3003000 time. For example, in a specific embodiment of the invention, the sequencing depth is 1000, i.e. the specific PCR amplified product is sequenced for 1000 times.
In the present invention, when the DNA molecules for detection are from various samples, each sample can be provided with a different barcode so as to be differentiated during sequencing process (Micah Hamady, Jeffrey J Walker, J Kirk Harris et al. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature Methods, 2008, 5(3)), enabling sequencing of various samples at the same time.
In the present invention, the genome reference sequence may be obtained from public database. For example, the human genome sequence may be human genome reference sequence in NCBI or ucsc database.
In the present invention, the sequence alignment may be done with any sequence alignment program, for example, Torrent Mapping Alignment Program (TMAP) and BWA (Burrow-Wheeler-Aligner) available to a person skilled in the art can be used to perform alignment and the reads is aligned with reference genome sequence to give the location of the reads at the reference genome sequence.
In the present invention, Torrent_Server_4.0_VM software is used on raw data generated by PGM sequencer to remove linker sequence and Tmap software is used for alignment to human hg19 reference genome, and haplotype SNP covering multiple and genotype are analyzed finally.
In a particular embodiment according to the invention, the detecting method comprises the steps of:
DNA extracting and sequencing: After extracting cell DNA with MDA whole genomic amplifying process (Qiagen Kit), the library is constructed according to Ion AmpliSeq™Library Kits 2.0 standard procedures. During this period, embryo MDA whole genomic amplification is amplified to DNA molecules concentrated as about 125˜275 bp through multiplex PCR. Two ends are added with linkers for sequencing, and each sample is provided with different barcode, thereby data of various samples obtained in data from one sequencing can be differentiated.
Alignment and statistics: Torrent_Server_4.0_VM software is used on raw data generated by PGM sequencer to remove linker sequence and Tmap software is used for alignment to human hg19 reference genome, and haplotype SNP covering multiple and genotype are analyzed finally.
The invention is useful for chromosomal Robertsonian translocation in preimplantation genetic diagnosis on suitable population, and is beneficial for providing genetic counseling and clinical decision basis. The invention is particularly suitable for detecting the condition that one of the parents is chromosomal Robertsonian translocation carrier and the other is normal karyotype, where normal embryo cannot be differentiated from chromosomal Robertsonian translocation carrying embryo according to conventional methods.
The following examples will be provided for detailed description which should not be construed as limitation thereto. The following examples are only parts of the invention, and based on the examples disclosed herein, a person skilled in the art can obtain all other examples which belong to the protection of the invention. Likewise, the accompanying figures are only those of some examples of the invention and based on the figures disclosed herein, a person skilled in the art can obtain all other figures which belong to the protection of the invention.
In case there is no specific description of the experimental conditions in the following examples, they were performed under conventional conditions or those recommended by the manufacture.
I. Materials
Sample sources: 8 embryo blastula stage trophoblast cell whole genomic amplified products and parental peripheral blood cell DNA samples, the father carries chromosomal Robertsonian translocation in Chromosome 13 and Chromosome 14 while the mother has normal chromosome karyotype. Analysis results of embryo chromosome copy number are shown in Table 6.
II. Procedures
1. Library Constructing and Sequencing
The library was constructed according to Ion AmpliSeg™ Library Kits 2.0 standard Library construction procedures. Multiplex PCR reactions were performed with the primers in Table 1 and Table 2 and then DNA molecules of the amplified products were added with linkers at both ends for sequencing. Under certain conditions, the nucleic acid molecules were allowed to grow in clusters and sequencing were performed on Ion Torrent PGM to give DNA fragments sequences in target location with fragment lengths of 125 bp˜275 bp.
In this example, the sequencing were performed on the DNA samples obtained from the 8 embryo cells and full blood DNA samples obtained from both of the parents according to official sequencing instruction by Ion Torrent.
2. Data Analysis
Torrent_Server_4.0_VM software was used on raw data generated by PGM sequencing to remove linker sequence and Tmap software is used for alignment to human hg19 reference genome. The sequences with low quality were removed and sequencing depth N of target sites were counted and the sites with N<100 were removed. All sequence directions and ratios of each of the bases at valid sites were analyzed. The base type that forward and reverse sequence number >20% and base ratios >10% was designated as one genotype of the site (X, X={A, T, C, G}).
Individual haplotype was speculated with genotypes of the parents and the embryo; while the valid site was the site providing valid SNP information for constructing pedigree haplotype and was generally the site in which one of the parents and the embryo is heterozygous. For the genotypes of the parents, ({X1X1}, {X2X2}), ({X1X1}, {X1X1}) was invalid site, ({X1X1}, {X1X2}) was valid site and ({X1X2}, {X1X2}) was verifiable site. According to valid site and verifiable site, haplotypes of parent and each of embryos were deduced. Male parent (LH), haplotypes of Chromosome 13 and Chromosome 14 were Aa and Bb, respectively and female parent (YT), haplotypes of Chromosome 13 and Chromosome 14 were Cc and Dd, respectively.
III. Results Analysis
Pedigree haplotype was built according to 115 SNP sites in target location (57 and 58 for Chromosome 13 and Chromosome 14, respectively) (results were shown in
According to the information that LH was translocation carrier and No. 3 embryo had Chromosome 14 duplication, it can be deduced that the Chromosome 13 haplotype from LH (A type) carried by No. 3 embryo was translocation chromosome haplotype. Further, according to other embryo carrying A type or a type, it can be deduced that B type in Chromosome 14 was translocation chromosome haplotype. Accordingly, it can be determined that No. 1, 4, 5 embryos carrying Chromosome 13 a type and Chromosome 14 b type were normal embryos; No. 2, 6, 7, 8 embryos carrying Chromosome 13 A type and Chromosome 14 B type were translocation carrying embryos.
I. Materials
Sample sources: 6 embryo blastula stage trophoblast cell whole genomic amplified products and parental peripheral blood cell DNA samples, the father carries chromosomal Robertsonian translocation in Chromosome 13 and Chromosome 14 (JXD) while the mother has normal chromosome karyotype (HCC). Analysis results of embryo chromosome copy number are shown in Table 8.
II. Procedures
1. Library Constructing and Sequencing
The library was constructed according to Ion AmpliSeq™ Library Kits 2.0 standard Library construction procedures. Multiplex PCR reactions were performed with the primers in Table 1 and Table 2 and then DNA molecules of the amplified products were added with linkers at both ends for sequencing. Under certain conditions, the nucleic acid molecules were allowed to grow in clusters and sequencing were performed on Ion Torrent PGM to give DNA fragments sequences in target location with fragment lengths of 125 bp˜275 bp.
In this example, the sequencing were performed on the DNA samples obtained from the 6 embryo cells and full blood DNA obtained from both of the parents according to official sequencing instruction by Ion Torrent.
2. Data Analysis
Torrent_Server_4.0_VM software was used on raw data generated by PGM sequencing to remove linker sequence and Tmap software is used for alignment to human hg19 reference genome. The sequences with low quality were removed and sequencing depth N of target sites were counted and the sites with N<100 were removed. All sequence directions and ratios of each of the bases at valid sites were analyzed. The base type that forward and reverse sequence number >20% and base ratios >10% was designated as one genotype of the site (X, X={A, T, C, G}).
Individual haplotype was speculated with genotypes of the parents and the embryo; while the valid site was the site that providing valid SNP information for constructing pedigree haplotype and was generally the site in which one of the parents and the embryo is heterozygous. For the genotypes of the parents, ({X1X1}, {X2X2}), ({X1X1}, {X1X1}) was invalid site, ({X1X1}, {X1X2}) was valid site and ({X1X2}, {X1X2}) was verifiable site. According to valid site and verifiable site, haplotypes of parent and each of embryos were deduced.
Female parent (HCC), haplotypes of Chromosome 13 and Chromosome 14 were Cc and Dd, respectively and male parent (JXD), haplotypes of Chromosome 13 and Chromosome 14 were Aa and Bb, respectively.
III. Results Analysis
Pedigree haplotype was built according to 115 SNP sites in target location (57 and 58 for Chromosome 13 and Chromosome 14, respectively) (results were shown in
According to the information that JXD is translocation carrier and No. 2 embryo had Chromosome 13 deletion, it can be deduced that the Chromosome 14 haplotype from JXD (b type) carried by No. 2 embryo was normal chromosome haplotype, i.e. Chromosome 14 B type was translocation chromosome haplotype. Further, according to other embryo carrying B type or b type, it can be deduced that A type in Chromosome 13 was translocation chromosome haplotype. Accordingly, it can be determined that No. 1, 4 embryos carrying Chromosome 14 B type and Chromosome 13 A type were translocation carrier embryos; No. 3, 6 embryos carrying Chromosome 14 b type and Chromosome 13 a type were normal embryos. No result was detected for No. 5 embryo chromosome copy number analysis and there was no valid sequence for this detection.
The invention is useful for embryo chromosomal translocation analysis on suitable population, and is beneficial for providing genetic counseling and clinical decision basis. A preimplantation genetic diagnosis can effectively prevent children patients from birth.
The suitable population according to the invention may be chromosomal Robertsonian translocation carriers determined by routine chromosome karyotype analysis.
The invention is not limited to the best embodiments as listed above. Anybody can achieve other products in various forms under the inspiration of the invention. The technical solution, no matter changes to the shape or structure, which is similar or identical to the invention, falls within the protection scope of the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CN2016/070696 | 1/19/2016 | WO | 00 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2017/124214 | 7/27/2017 | WO | A |
| Number | Name | Date | Kind |
|---|---|---|---|
| 20080243398 | Rabinowitz | Oct 2008 | A1 |
| Number | Date | Country |
|---|---|---|
| 105543372 | May 2016 | CN |
| Entry |
|---|
| Tan (Human Reproduction, vol. 28, No. 9 pp. 2581-2592, 2013). |
| The World Intellectual Property Organization (WIPO) International Search Report for PCT/CN2016/070696 dated Oct. 19, 2016 8 Pages. |
| Nathan, R.T. et al., “Use of Single Nucleotide Polymorphism Microarrays to Distinguish 1-23 between Balanced and Normal Chromosomes in Embryos from A Translocation Carrier”, Fertility and Sterility, vol. 96, No. 1, Jul. 31, 2011, ISSN: e58-e65, abstract, and the section of materials and methods. |
| Zhang, Fan, Chromosome Disease and Diagnosis, Dec. 31, 2006, 1-23 figures 3-6, and p. 42. |
| Number | Date | Country | |
|---|---|---|---|
| 20190032119 A1 | Jan 2019 | US |
