"Clinical outcome of preimplantation genetic diagnosis and screening using next generation sequencing", Tan et al 2014; of course, you can do a lot more with SNP arrays than just look for gross abnormalities / avoid birth defects...
Pointer from http://infoproc.blogspot.com/2014/12/preimplantation-genetic-diagnosis-and.html ; excerpts:
"A total of 395 couples participated. They were carriers of either translocation or inversion mutations, or were patients with recurrent miscarriage and/or advanced maternal age. A total of 1,512 blastocysts were biopsied on D5 after fertilization, with 1,058 blastocysts set aside for SNP array testing and 454 blastocysts for NGS testing. In the NGS cycles group, the implantation, clinical pregnancy and miscarriage rates were 52.6% (60/114), 61.3% (49/80) and 14.3% (7/49), respectively. In the SNP array cycles group, the implantation, clinical pregnancy and miscarriage rates were 47.6% (139/292), 56.7% (115/203) and 14.8% (17/115), respectively. The outcome measures of both the NGS and SNP array cycles were the same with insignificant differences. There were 150 blastocysts that underwent both NGS and SNP array analysis, of which seven blastocysts were found with inconsistent signals. All other signals obtained from NGS analysis were confirmed to be accurate by validation with qPCR. The relative copy number of mitochondrial DNA (mtDNA) for each blastocyst that underwent NGS testing was evaluated, and a significant difference was found between the copy number of mtDNA for the euploid and the chromosomally abnormal blastocysts. So far, out of 42 ongoing pregnancies, 24 babies were born in NGS cycles; all of these babies are healthy and free of any developmental problems.
Chromosomal abnormalities, including numerical errors and structural anomalies, are widespread in human embryos produced in vitro [1], and the incidence increases dramatically in embryos with advancing maternal age [2-4]. Chromosomal abnormalities are a main reason for spontaneous abortions [5,6], and repeated implantation failures after transfer of in vitro produced embryos [7]. Furthermore, embryos from carriers of balanced translocations [8,9] are at particularly high risk of chromosomal abnormalities. Previous papers have been published about the application of preimplantation genetic screening (PGS) in cases with advanced maternal age [10,11] or recurrent pregnancy loss [12], and the application of preimplantation genetic diagnosis (PGD) in carriers of translocations [13]. Thus, PGD/PGS and the selection of chromosomally normal embryos for transfer should be an effective approach to improve live birth rate, as well as reduce spontaneous abortion and birth defects. Studies were performed using blastocyst biopsy [14] and either fluorescence in situ hybridization (FISH) [15], comparative genomic hybridization (CGH) [16-18] or array based methods, such as array-CGH [13,19,20] and single-nucleotide polymorphism array (SNP array) [21-24] for sample analysis...Array based techniques (aCGH and SNP array) have been used to screen all 24 human chromosomes. However, array-based methods are still relatively expensive, restricting their clinical applications. Next generation sequencing (NGS) has now become cost-effective, and this precise and comprehensive genetic analysis tool is being increasingly used in human medicine including noninvasive prenatal diagnosis [25], and there is increasing interest for its application in PGD/PGS as well.
A total of 395 couples were subjected to in vitro fertilization-preimplantation genetic diagnosis (IVF-PGD) treatment, including 129 couples with a NGS-based test and 266 couples with a SNP array-based test, for the detection of embryonic chromosomal abnormalities. The NGS test was performed using low coverage whole-genome sequencing with a HiSeq 2000 platform. The SNP array test was performed using Affymetrix Gene Chip Mapping Nsp I 262 K. The average age of the patients was 32.1 years (with an age range of 20–44 years). In the NGS cycles group, 84 patients were confirmed to have a chromosomally abnormal karyotype; 18 of which had a Robertsonian translocation, 59 had a reciprocal translocation, and 7 patients had a inversion. Another 45 couples were included because of an advanced maternal age (AMA; ≥38 years) and/or recurrent miscarriage (RM; ≥2). In the SNP array cycles group, 213 patients (of which 58 had a Robertsonian translocation, 144 had a reciprocal translocation, 11 had an inversion) and another 57 couples with AMA and/or RM were included. A total of 1,512 blastocysts were obtained, with 454 blastocysts for NGS testing and 1,058 blastocysts for SNP array analysis. In addition, 150 blastocysts from the 454 blastocysts were subjected to both NGS and SNP array tests, and blastocysts with inconsistent results would be further validated by qPCR.
Of the 1,058 blastocysts with SNP array analysis, 468 (44.2%) euploid and 590 (55.8%) chromosomally abnormal blastocysts were identified, 189 blastocysts had numerical chromosome aberrations, 298 contained imbalanced structural aberrations and 103 blastocysts were detected with both numerical and imbalanced structural aberrations. The median number of normal/balanced embryos per couple was 1.76 (range from 0 to 8). The group of reciprocal translocation carriers obtained 40.8% (247/606) embryos with imbalanced aberrations. Normal/balanced embryos constituted 60.2% (106/176) of the cohort in couples with AMA and/or RM (Table 2).
Among the 129 couples in the NGS cycles group, 33 couples had no euploid embryos suitable for transfer; 75 couples underwent embryo transfer and the remaining 21 couples are currently still waiting for transfer. In the SNP array cycles group, 177 couples underwent embryo transfer, 66 couples had no suitable embryos for transfer, and 23 couples are currently still waiting.
Of the 666 normal/balanced blastocysts, 421 blastocysts were warmed after vitrification, 406 survived (96.4% of survival rate) and were transferred in 283 cycles. The numbers of blastocysts transferred per cycle were 1.425 (114/80) and 1.438 (292/203) for NGS and SNP array, respectively. The proportion of transferred embryos that successfully implanted was evaluated by ultrasound 6–7 weeks after embryo transfer, indicating that 60 and 139 embryos resulted in a fetal sac, giving implantation rates of 52.6% (60/114) and 47.6% (139/292) for NGS and SNP array, respectively. Prenatal diagnosis with karyotyping of amniocentesis fluid samples did not find any fetus with chromosomal abnormalities. A total of 164 pregnancies were detected, with 129 singletons and 35 twins. The clinical pregnancy rate per transfer cycle was 61.3% (49/80) and 56.7% (115/203) for NGS and SNP array, respectively (Table 3). A total of 24 miscarriages were detected, giving rates of 14.3% (7/49) and 14.8% (17/115) in NGS and SNP array cycles, respectively. In NGS cycles group, four miscarriages were spontaneous abortions occurred in early pregnancy, and the other three were artificial abortions with two caused by embryo diapause and another one caused by extrauterine (cervical) implantation. In the SNP array cycles group, 12 spontaneous abortions in early pregnancy and five artificial abortions occurred. Testing of the miscarried tissue by comparative genomic hybridization (CGH) revealed that the miscarried embryos in both NGS and SNP array cycles were chromosomally normal. The ongoing pregnancy rates were 52.5% (42/80) and 48.3% (98/203) in NGS and SNP array cycles, respectively. Out of these pregnancies, 24 babies were delivered in 20 NGS cycles; so far, all the babies are healthy and chromosomally normal according to karyotype analysis. In the SNP array cycles group the outcome of all pregnancies went to full term and 75 healthy babies were delivered (Table 3).
Twenty-four babies were born, so far, all of them healthy, indicating the accuracy of NGS as well as the safety of blastocyst biopsy and vitrification. It illustrates that NGS-PGD is applicable for the genetically high-risk populations, such as carriers of Robertsonian translocations and reciprocal translocations."
Pointer from http://infoproc.blogspot.com/2014/12/preimplantation-genetic-diagnosis-and.html ; excerpts:
"A total of 395 couples participated. They were carriers of either translocation or inversion mutations, or were patients with recurrent miscarriage and/or advanced maternal age. A total of 1,512 blastocysts were biopsied on D5 after fertilization, with 1,058 blastocysts set aside for SNP array testing and 454 blastocysts for NGS testing. In the NGS cycles group, the implantation, clinical pregnancy and miscarriage rates were 52.6% (60/114), 61.3% (49/80) and 14.3% (7/49), respectively. In the SNP array cycles group, the implantation, clinical pregnancy and miscarriage rates were 47.6% (139/292), 56.7% (115/203) and 14.8% (17/115), respectively. The outcome measures of both the NGS and SNP array cycles were the same with insignificant differences. There were 150 blastocysts that underwent both NGS and SNP array analysis, of which seven blastocysts were found with inconsistent signals. All other signals obtained from NGS analysis were confirmed to be accurate by validation with qPCR. The relative copy number of mitochondrial DNA (mtDNA) for each blastocyst that underwent NGS testing was evaluated, and a significant difference was found between the copy number of mtDNA for the euploid and the chromosomally abnormal blastocysts. So far, out of 42 ongoing pregnancies, 24 babies were born in NGS cycles; all of these babies are healthy and free of any developmental problems.
Chromosomal abnormalities, including numerical errors and structural anomalies, are widespread in human embryos produced in vitro [1], and the incidence increases dramatically in embryos with advancing maternal age [2-4]. Chromosomal abnormalities are a main reason for spontaneous abortions [5,6], and repeated implantation failures after transfer of in vitro produced embryos [7]. Furthermore, embryos from carriers of balanced translocations [8,9] are at particularly high risk of chromosomal abnormalities. Previous papers have been published about the application of preimplantation genetic screening (PGS) in cases with advanced maternal age [10,11] or recurrent pregnancy loss [12], and the application of preimplantation genetic diagnosis (PGD) in carriers of translocations [13]. Thus, PGD/PGS and the selection of chromosomally normal embryos for transfer should be an effective approach to improve live birth rate, as well as reduce spontaneous abortion and birth defects. Studies were performed using blastocyst biopsy [14] and either fluorescence in situ hybridization (FISH) [15], comparative genomic hybridization (CGH) [16-18] or array based methods, such as array-CGH [13,19,20] and single-nucleotide polymorphism array (SNP array) [21-24] for sample analysis...Array based techniques (aCGH and SNP array) have been used to screen all 24 human chromosomes. However, array-based methods are still relatively expensive, restricting their clinical applications. Next generation sequencing (NGS) has now become cost-effective, and this precise and comprehensive genetic analysis tool is being increasingly used in human medicine including noninvasive prenatal diagnosis [25], and there is increasing interest for its application in PGD/PGS as well.
A total of 395 couples were subjected to in vitro fertilization-preimplantation genetic diagnosis (IVF-PGD) treatment, including 129 couples with a NGS-based test and 266 couples with a SNP array-based test, for the detection of embryonic chromosomal abnormalities. The NGS test was performed using low coverage whole-genome sequencing with a HiSeq 2000 platform. The SNP array test was performed using Affymetrix Gene Chip Mapping Nsp I 262 K. The average age of the patients was 32.1 years (with an age range of 20–44 years). In the NGS cycles group, 84 patients were confirmed to have a chromosomally abnormal karyotype; 18 of which had a Robertsonian translocation, 59 had a reciprocal translocation, and 7 patients had a inversion. Another 45 couples were included because of an advanced maternal age (AMA; ≥38 years) and/or recurrent miscarriage (RM; ≥2). In the SNP array cycles group, 213 patients (of which 58 had a Robertsonian translocation, 144 had a reciprocal translocation, 11 had an inversion) and another 57 couples with AMA and/or RM were included. A total of 1,512 blastocysts were obtained, with 454 blastocysts for NGS testing and 1,058 blastocysts for SNP array analysis. In addition, 150 blastocysts from the 454 blastocysts were subjected to both NGS and SNP array tests, and blastocysts with inconsistent results would be further validated by qPCR.
Of the 1,058 blastocysts with SNP array analysis, 468 (44.2%) euploid and 590 (55.8%) chromosomally abnormal blastocysts were identified, 189 blastocysts had numerical chromosome aberrations, 298 contained imbalanced structural aberrations and 103 blastocysts were detected with both numerical and imbalanced structural aberrations. The median number of normal/balanced embryos per couple was 1.76 (range from 0 to 8). The group of reciprocal translocation carriers obtained 40.8% (247/606) embryos with imbalanced aberrations. Normal/balanced embryos constituted 60.2% (106/176) of the cohort in couples with AMA and/or RM (Table 2).
Among the 129 couples in the NGS cycles group, 33 couples had no euploid embryos suitable for transfer; 75 couples underwent embryo transfer and the remaining 21 couples are currently still waiting for transfer. In the SNP array cycles group, 177 couples underwent embryo transfer, 66 couples had no suitable embryos for transfer, and 23 couples are currently still waiting.
Of the 666 normal/balanced blastocysts, 421 blastocysts were warmed after vitrification, 406 survived (96.4% of survival rate) and were transferred in 283 cycles. The numbers of blastocysts transferred per cycle were 1.425 (114/80) and 1.438 (292/203) for NGS and SNP array, respectively. The proportion of transferred embryos that successfully implanted was evaluated by ultrasound 6–7 weeks after embryo transfer, indicating that 60 and 139 embryos resulted in a fetal sac, giving implantation rates of 52.6% (60/114) and 47.6% (139/292) for NGS and SNP array, respectively. Prenatal diagnosis with karyotyping of amniocentesis fluid samples did not find any fetus with chromosomal abnormalities. A total of 164 pregnancies were detected, with 129 singletons and 35 twins. The clinical pregnancy rate per transfer cycle was 61.3% (49/80) and 56.7% (115/203) for NGS and SNP array, respectively (Table 3). A total of 24 miscarriages were detected, giving rates of 14.3% (7/49) and 14.8% (17/115) in NGS and SNP array cycles, respectively. In NGS cycles group, four miscarriages were spontaneous abortions occurred in early pregnancy, and the other three were artificial abortions with two caused by embryo diapause and another one caused by extrauterine (cervical) implantation. In the SNP array cycles group, 12 spontaneous abortions in early pregnancy and five artificial abortions occurred. Testing of the miscarried tissue by comparative genomic hybridization (CGH) revealed that the miscarried embryos in both NGS and SNP array cycles were chromosomally normal. The ongoing pregnancy rates were 52.5% (42/80) and 48.3% (98/203) in NGS and SNP array cycles, respectively. Out of these pregnancies, 24 babies were delivered in 20 NGS cycles; so far, all the babies are healthy and chromosomally normal according to karyotype analysis. In the SNP array cycles group the outcome of all pregnancies went to full term and 75 healthy babies were delivered (Table 3).
Twenty-four babies were born, so far, all of them healthy, indicating the accuracy of NGS as well as the safety of blastocyst biopsy and vitrification. It illustrates that NGS-PGD is applicable for the genetically high-risk populations, such as carriers of Robertsonian translocations and reciprocal translocations."
6w
