Improved assay performance of single nucleotide polymorphism array over conventional karyotyping in analyzing products of conception.

BACKGROUND: Conventional karyotyping has been a routine method to identify chromosome abnormalities in products of conception. However, this process is being transformed by single nucleotide polymorphism (SNP) array, which has advantages over karyotyping, including higher resolution and dispensing with cell culture. Therefore, the purpose of this study was to evaluate the advantage of high-resolution SNP array in identifying genetic aberrations in products of conception. METHODS: We consecutively collected 155 products of conception specimens, including 139 from first-trimester miscarriage and 16 from second-trimester miscarriage. SNP array was performed on these samples in parallel with G-banded karyotyping. RESULTS: The test success rate was 98.1% (152/155) using SNP array, which was higher than that using karyotyping (133/155, 85.8%). It yielded a 63.8% (97/152) abnormality rate, and the frequency of various chromosome abnormalities was in agreement with other previous studies. The results between array and karyotyping demonstrated a 94.0% (125/133) concordance. SNP array obtained additional aberrations in 3.8% (5/133) of those cases unidentified by karyotyping, which included three cases with whole-genome uniparental disomy, one with pathogenic copy number variation, and one with del(4)(q35.1q35.2) and dup(12)(q24.31q24.33). However, chromosome translocations presented in two cases and tetraploidy presented in one case were detected by karyotyping instead of array. Additionally, two out of three cases with mosaic trisomy were revealed by array but recognized as pure trisomy by karyotyping. CONCLUSION: This study demonstrated that SNP array had certain advantages over G-banded karyotyping, including a higher success rate, additional detection of copy number variations and uniparental disomy, and improved sensitivity to mosaicism. Therefore, it would be an alternative method to karyotyping in clinical genetic practice.

[Investigation of ultrasound markers in screening fetal trisomy 21].

OBJECTIVE: To investigate the clinical value of ultrasound markers in screening fetal trisomy 21. METHODS: From Jan. 2001 to Dec. 2011, a retrospective study about sonographic information of 138 fetuses diagnosed as trisomy 21 was taken in the First Affiliated Hospital of Sun Yat-sen University. All fetuses were divided into 3 groups: isolated ultrasound markers, non-isolated ultrasound markers, and isolated structural malformations or other abnormalities. The relationship between trisomy 21 and ultrasound markers as well as structural anomalies or other abnormalities was analyzed. RESULTS: Sonographic anomalies were detected in 132 fetuses (95.7%, 132/138), including ultrasound markers and structural malformations or other abnormalities. One hundred and twenty cases (87.0%, 120/138) had ultrasound markers, 38 (31.7%, 38/120) had one marker and 82 (68.3%, 82/120) had more than one marker (P < 0.01). Fifty-one fetuses (37.0%, 51/138) had isolated ultrasound markers and non-isolated markers were found in 69 fetuses (50.0%, 69/138). Only 12 fetuses (8.7%, 12/138) had isolated structural malformations or other abnormalities. In 20 fetuses on whom the first-trimester ultrasound screening were performed, all had ultrasound markers, 95% (19/20) had thickened nuchal translucency and 55% (11/20) had nasal bone hypoplasia. The most common ultrasound markers on the second-trimester screening were nasal bone hypoplasia, which accounted for 41.9% (52/124) cases, followed by thickened nuchal fold (25.0%, 31/124), short femurs and humerus (24.2%, 30/124), echogenic intracardiac focus (16.1%, 20/124), mild ventriculomegaly (15.3%, 19/124), hyperechoic bowel (12.9%, 16/124), mild renal pyelectasis (12.1%, 15/124). Furthermore, the common structural malformations or other abnormalities were as follows: cardiac defects (33.1%, 41/124), digestive system (26.6%, 33/124). CONCLUSIONS: Ultrasound markers are valuable for screening fetal trisomy 21. The fetuses of trisomy 21 usually had more than one ultrasound markers or associated with other abnormalities. Combinations of ultrasound markers with the results of serum screening and maternal age are necessary for evaluation.

[Spectral karyotyping of seven prenatally detected marker chromosomes and complex chromosome aberrations].

OBJECTIVE: To perform spectral karyotyping (SKY), fluorescence in situ hybridization (FISH) and conventional karyotyping on prenatally detected marker chromosomes and complex chromosomal aberrations. METHODS: Five marker chromosomes and 2 complex chromosome aberrations diagnosed by G banding were collected. SKY was performed to verify the composition of marker chromosomes. FISH was used to confirm the diagnosis when necessary. In certain cases, C or N banding technique was employed to verify the composition of chromosomes. Results of ultrasonography and pregnancy outcome were reviewed. RESULTS: Among the 5 marker chromosomes, 2 were large and 3 were medium in size, 4 were de novo and one was inherited from the father. By SKY analysis, 2 marker chromosomes have originated from non-acrocentric chromosomes (4 and 9), whilst the other two have originated from acrocentric chromosomes (21 and 22). The remainder was derived from X chromosome. The SKY results were confirmed by FISH in 3 cases. Four cases have chosen to terminate the pregnancy after genetic counseling. A fetus with inherited paternal marker chromosome was delivered at term, and showed normal development during the first year of life. As for the other 2 cases with complex chromosome aberrations, by SKY examination, one had duplication in chromosome 8 and the other had chromosome rearrangements derived from translocation between chromosomes 2 and 6. In the latter case the fetus was delivered at term but showed developmental retardation at 6 months. CONCLUSION: SKY in combination with FISH can facilitate identification of the origins of marker chromosomes as well as complex chromosomal aberrations. With combined information from ultrasonography, SKY and FISH, effective counseling may be offered to the patients.

[Clinical features of abnormal chromosome karyotypes in twin pregnancies complicated with structural abnormalities].

OBJECTIVE: To investigate the clinical features of the abnormal chromosome karyotypes in twin pregnancies complicated with fetal malformations. METHODS: Totally 181 twin pregnancies (362 fetuses) in which one or two fetuses had abnormalities diagnosed by ultrasound were referred to the First Affiliated Hospital of Sun Yat-Sen University from January, 2000 to September, 2010. They were divided into different groups according to (1) maternal age: the cases with maternal age ≥ 35 were divided into advanced pregnancy group (105 fetuses), and those with maternal age < 35 were divided into young pregnancy group (203 fetuses); (2) conceived method: those conceived by assisted reproductive technology were divided into assisted reproductive group (81 fetuses), and the natural conception pregnancies were divided into natural conception group (227 fetuses); (3) chorionicity: the monochorionic twin (MCT) pregnancies were divided into MCT group (123 fetuses), and the dichorionic twin (DCT) pregnancies were divided into DCT group (185 fetuses); (4) structural abnormalities: 205 fetuses with structural abnormalities were divided into the abnormal fetal group, and 103 fetuses without structural abnormalities were divided into the normal fetal group. All fetuses were examined by the ultrasound and chromosomes were examined in 308 fetuses. RESULTS: (1) The karyotype of fetuses: among 181 twin pregnancies, 23 cases had chromosomal abnormalities in 1 or 2 fetuses (12.7%, 23/181), and chromosomes were examined in both fetuses in 20 of 23 cases. Twenty-six of 308 fetuses were found with abnormal chromosomes (8.4%, 26/308), and the aneuploid was the most common type of abnormal karyotypes (53.8%, 14/26). Twenty-one of 205 fetuses with malformations were found with abnormal karyotypes (10.2%, 21/205). (2) Seven of 123 fetuses in MCT group were with abnormal karyotypes (5.7%, 7/123), and 19 of 185 fetuses in DCT group were with abnormal karyotypes (10.3%, 19/185). There was no statistical difference of abnormal chromosome incidence between the two groups. There were 14 fetuses with aneuploid in DCT group (7.6%, 14/185); but there was no fetus with aneuploid in MCT group. There was statistical difference between these two groups. In two cases of DCT group, only one fetus with malformation received chromosome examination because another fetus was dead, and the karyotypes were trisomy 21 and trisomy 18 respectively. Both fetuses of the rest 17 cases received chromosome examination, and the chromosomes of both fetuses in each pregnancy were different. Fifteen of 19 fetuses with abnormal chromosomes in DCT group were complicated with structural abnormalities, and 7 fetuses of 4 twin pregnancies in MCT group were with chromosomal abnormalities. (3) The comparison of the abnormal karyotype incidence between the advanced pregnancy group and young pregnancy group: the abnormal karyotype incidence of the advanced pregnancy group was 7.6% (8/105), and that was 8.9% (18/203) in young pregnancy group. There was no statistical difference between the two groups (P > 0.05). Six of 105 fetuses in advanced pregnancy group were aneuploids (5.7%, 6/105), and 8 of 203 fetuses in young pregnancy group were aneuploids (3.9%, 8/203). The aneuploid incidence in advanced pregnancy group was significantly higher than that in young pregnancy group (P < 0.05).(4) The comparison of the abnormal karyotype incidence between the assisted reproductive group and the natural conception group: 11 of 81 fetuses were with the abnormal karyotypes in assisted reproductive group (13.6%, 11/81), and 15 of 227 fetuses were with the abnormal karyotypes in assisted reproductive group (6.6%, 15/227). There was statistical difference between the two groups (P < 0.05). There were 7 fetuses with the aneuploid in assisted reproductive group (8.6%, 7/81) and 7 fetuses with the aneuploid in natural conception group (3.1%, 7/227), which showed no statistical difference (P > 0.05). (5) The comparison of the abnormal karyotype incidence between the abnormal fetal group and normal fetal group: 21 of 205 fetuses in abnormal fetal group were with abnormal karyotypes (10.2%, 21/205), and 5 of 103 fetuses in normal fetal group were with abnormal karyotypes (4.9%, 5/103). There was no statistical difference (P > 0.05). 13 fetuses in abnormal fetal group were with the aneuploid (6.3%, 13/205), and only one fetus in normal fetal group was aneuploid (1.0%, 1/103). There was statistical difference between the two groups (P < 0.05). CONCLUSIONS: Aneuploid is the most common abnormal karyotype in twin pregnancy complicated with fetal abnormalities, especially trisomy 21. Aneuploid mainly occurs in only one fetus of DCT, and chromosomal discordance is usually found in DCT. While in MCT, the twin fetuses with the same abnormal karyotype may have different phenotypes. The results suggest that it is necessary to analyze both karyotypes of twins even if only one fetus is complicated with structural abnormalities.

[Combined use of molecular cytogenetic techniques to detect a small chromosomal translocation].

OBJECTIVE: Comprehensive use of molecular cytogenetic techniques for the detection of 1 case of small chromosome translocation. METHODS: Following conventional chromosome preparation, G-banding karyotype analysis, spectral karyotyping (SKY), whole chromosome painting, two-color fluorescence in situ hybridization (FISH) and subtelomeric probe FISH were performed. RESULTS: G-banded karyotype was 46, XX, ?(22q11.3), SKY karyotype analysis was 46, XX, der (4)t(4;6) and found no abnormalities on chromosome 22, staining signal was not found with any abnormalities on chromosome 6. Two-color FISH indicated a chromosomal translocation segment of 22q13.3 to one end of the short arm of chromosome 4. Subtelomeric FISH probe showed the end of the long arm of chromosome 22 and the end of the short arm of chromosome 4 reciprocal translocation. High resolution G-banding and FISH result indicated 46, XX, t(4;22)(p15.3;q13.2). CONCLUSION: The testing of small chromosomal translocation should be combined with clinical information and integrated use of molecular cytogenetic techniques to improve the accuracy of diagnosis of chromosomal diseases.

[Genetic analysis of chorionic villi specimen in spontaneous abortion using various methods].

OBJECTIVE: To explore the efficacy of multiplex ligation-dependent probe amplification (MLPA) combined with fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) combined with FISH in genetic analysis of chorionic villi specimen (CVS) of spontaneous abortion. METHODS: CGH + FISH and MLPA + FISH were used for genetic analysis of 29 CVS from spontaneous abortion and 6 normal CVS from selective abortion, in the mean time, those results were compared with conventional cytogenetic karyotyping. RESULTS: The report time were 40 hours in MLPA + FISH and 120 hours in CGH + FISH. The mean time of chorionic villi culture was (240 +/- 72) hours. The successful rate of specimen analysis were 97% (34/35) in CGH, 100% (35/35) in MLPA, 100% (35/35) in FISH and 91% (32/35) in conventional cytogenetic karyotyping. Apart from 1 case failed in CGH analysis, the results from MLPA + FISH were almost similar to that from CGH + FISH, however, that 1 specimen failed in CGH were detected successfully by MLPA + FISH. The discrepancy rate were 13% (4/31) in CGH + FISH and 12% (4/32) in MLPA + FISH respectively when compared with conventional cytogenetic analysis. CONCLUSIONS: MLPA + FISH analysis present shorter detecting time and achieve 100% rate of successful report. This combined method was an important adjuvant approach to conventional cytogenetic karyotyping in CVS from spontaneous abortion.

[Prenatal diagnosis of achondroplasia].

OBJECTIVE: To diagnose achondroplasia prenatally by FGFR3 gene detection. METHODS: Seventy-eight fetuses affected by short-limb dysplasias were recruited. Umbilical blood sampling was employed to obtain fetal blood for karyotyping and FGFR3 gene detection. Genomic DNA was extracted, and the exon 10 of the FGFR3 gene was amplified. PCR amplicons were analyzed by DNA sequencing and restriction fragment length polymorphism with Bfm I. The FGFR3 exon 10 from the parents of the positive fetuses was screened by the same method. RESULTS: In 78 fetuses affected with short-limb dysplasias, 8 cases had G1138A heterozygotic mutation and normal karyotype, and were diagnosed as achondroplasia. The other 70 fetuses had normal nucleotide at nucleotide 1138 in exon 10 of FGFR3, therefore were excluded from achondroplasia. Only one father in parents of the 8 achondroplasia fetuses also had the G1138A mutation. CONCLUSION: Achondroplasia could be diagnosed prenatally in the fetuses affected with short-limb dysplasias by using PCR-RFLP and DNA sequencing of the exon 10 of the FGFR3 gene.