Errors during in vitro fertilization (IVF) workflows pose significant risks; yet, existing quality control measures remain insufficient. Herein, we developed a preimplantation full-sibling relationship identification (PFSRI) model using ultra-low-depth whole genome sequencing (uldWGS) data from 789 biopsied embryos (average depth, 0.02×). The model predicts embryonic relationships via the heterozygosity-based relationship ratio (HetRR). In double-blind testing, PFSRI successfully distinguished full-sibling embryos from different ovarian stimulation cycles within the same family and identified resequenced samples. At optimized thresholds (unique reads [URs] ≥ 800 K and co-detected SNPs [CoSNPs] ≥ 800), the model achieved 100% accuracy in discriminating full-sibling, unrelated, and identical relationships, with performance unaffected by chromosomal status. The PFSRI model provides a cost-effective and robust tool for precise embryo relationship identification, serving as a valuable quality control instrument for IVF laboratories.

Inverted duplication of the short arm of chromosome 8 (inv dup del (8p)) and the deletion of its adjacent terminal represent a rare chromosomal rearrangement. To date, only a limited number of prenatal cases have been documented from a molecular cytogenetic perspective. This study investigates the molecular genetic characteristics and intrauterine ultrasound phenotypes of fetuses prenatally diagnosed with inv dup del (8p). We retrospectively analyzed chromosomal microarray analysis (CMA) results from cases seeking prenatal diagnosis at the Medical Genetics Center of Guangdong Women and Children’s Hospital from January 2016 to December 2022. We identified 12 prenatal cases of inv dup del (8p) and summarized their prenatal clinical manifestations and associated genes by combining ultrasound findings with literature review. Both G-banding and CMA techniques confirmed the presence of interstitial duplication with concomitant terminal deletion of chromosome 8’s short arm in all 12 cases. The locations and lengths of the 8p duplications varied in their proximal breakpoint. Observed ultrasound findings included fetal increased nuchal translucency (NT), lateral cerebral ventricular dilatation, craniofacial dysmorphisms and abnormalities of the brain, heart and kidneys. Ectopic recombination appears to be the dominant mechanism for rearrangement formation in cases 1–11. In contrast, case 12 exhibited inv dup del (8p) without an intact region between duplication and deletion, which is better explained by the U-type exchange mechanism. The intrauterine phenotypes of inv dup del (8p) are diverse, with cerebral and cardiac anomalies being the most commonly observed ultrasound findings. However, these clinical manifestations are not specific to inv dup del (8p), and some fetuses may not exhibit noticeable ultrasound abnormalities during early gestation. Therefore, definitive diagnostic testing through karyotyping and CMA is essential. Additionally, CMA enables precise detection of copy number variations (CNVs), including exact size and genomic location. This detailed information is critical for accurate genetic counselling and helps clarify the mechanism behind the inv dup (8p) rearrangement.

目的 分析无创DNA产前检测(NIPT)在胎儿染色体非整倍体疾病及染色体拷贝数变异筛查中的临床应用.方法 选取2015年1月至2018年12月在广东省惠州市第一妇幼保健院产前诊断中心进行NIPT的9331例孕妇作为研究对象,对NIPT提示高风险孕妇进行介入性产前诊断,抽取羊水或脐血进行染色体核型分析及染色体微阵列分析,并分析NIPT与介入性产前诊断结果的符合情况.结果 9331例孕妇中进行NIPT提示染色体异常高风险245例(2.63％),其中236例孕妇同意进行介入性产前诊断,其中21三体综合征高风险86例,确诊82例,阳性预测值为95.35％,假阳性率为0.04％;18三体综合征高风险25例,确诊16例,阳性预测值为64.00％,假阳性率为0.10％;13三体综合征高风险19例,确诊4例,阳性预测值为21.05％,假阳性率为0.16％;性染色体异常高风险45例,确诊19例,阳性预测值为42.22％,假阳性率为0.28％;其他常染色体异常高风险67例,提示染色体拷贝数变异,其中61例孕妇进一步产前诊断,检出与NIPT结果相符的拷贝数变异18例,阳性预测值为29.51％,假阳性率为0.46％.结论 NIPT对胎儿染色体非整倍体疾病及染色体拷贝数变异具有较高的检出率和较低的假阳性率,其在临床推广应用能有效减少染色体异常患儿的出生.

目的 应用染色体微阵列分析(CMA)技术在全基因组水平分析先天性心脏病(CHD)胎儿的遗传学病因,探索CMA技术在C H D胎儿致病基因检测中的临床应用价值.方法 选取216例经胎儿超声心动图确诊为C H D胎儿的羊水或者脐血标本进行常规染色体核型分析,所有标本同时增加CMA检测,应用相关生物信息学数据库对结果进行分析,并随访胎儿的妊娠结局.结果 在216例CHD胎儿中,染色体异常检出率为8.80％(19/216),CMA检测显示致病性染色体拷贝数变异(CNV)的检出率为14.35％(31/216).根据结构畸形情况分成3组:单一心脏结构畸形组(Ⅰ组91例)、多发心脏结构畸形组(Ⅱ组66例)、心内合并心外结构畸形组(Ⅲ组59例).3组胎儿染色体异常检出率分别为:Ⅰ组6.59％(6/91)、Ⅱ组9.09％(6/66)、Ⅲ组11.86％(7/59),差异无统计学意义(P>0.05);3组胎儿CMA致病性CNV检出率分别为:Ⅰ组8.79％(8/91)、Ⅱ组13.64％(9/66)、Ⅲ组23.73％(14/59),差异无统计学意义(P>0.05);在197例染色体正常的CHD胎儿中,CMA额外检测到14例异常,可将CHD胎儿的遗传学病因检出率提高7.11％.结论 在常规染色体核型分析基础上增加CMA检测,可以提高CHD胎儿的遗传学病因检出率,为评估CHD胎儿的远期预后提供科学依据.

With the extensive application of highly sensitive genetic techniques in the field of prenatal diagnosis, prenatal chromosomal mosaicisms including true fetal mosaicisms and confined placental mosaicisms are frequently identified in clinical settings, and the diagnostic criteria and principle of genetic counseling and clinical management for such cases may vary significantly among healthcare centers across the country. This not only has brought challenges to laboratory technician, genetic counselor and fetal medicine doctor, but can also cause confusion and anxiety of the pregnant woman and their family members. In this regard, we have formulated a consensus over the prenatal diagnosis and genetic counseling for chromosomal mosaicisms with the aim to promote more accurate and rational evaluation for fetal chromosomal mosaicisms in prenatal clinics.

Background The mosaic forms and clinical phenotypes of fetuses with isochromosome Y are difficult to predict. Therefore, we summarized the cases of nine fetuses with isochromosome Y identified in prenatal diagnosis with a combination of molecular cytogenetic techniques, providing clinical evidence for prenatal genetic counseling. Methods The prenatal diagnosis and pregnancy outcomes of nine fetuses with isochromosome Y were obtained by a retrospective analysis. Isochromosome Y was identified prenatally by different approaches, such as conventional karyotyping, chromosomal microarray analysis (CMA), quantitative fluorescent polymerase chain reaction (QF-PCR) and fluorescence in situ hybridization (FISH). Results Seven idic(Y) fetuses and two i(Y) fetuses were identified. One fetus was complete for i(Y)(p10), and the rest with 45,X had mosaic forms. A break and fusion locus was identified in Yp11.3 in one fetus, in Yq11.22 in six fetuses and in Yp10 in two fetuses. The CMA results suggested that different deletions and duplications were found on the Y chromosome. The deletion fragments ranged from 4.7 Mb to the entire Y chromosome, and the duplication fragments ranged from 10.4 to 18.0 Mb. QF-PCR analysis suggested that the AZF region was intact in one fetus, four fetuses had AZFb+c+d deletion, one fetus had AZFa+b+c+d deletion, and one fetus had AZFc+d deletion. Finally, four healthy male neonates were delivered successfully, but the parents of the remaining five fetuses, including three healthy and two unhealthy fetuses, chose to terminate their pregnancies. Conclusion The fetus and neonate phenotype of prenatally detected isochromosome Y usually is that of a normally developed male, ascertained in the absence of other indicators of a fetal structural anomaly. Our study provides clinical reference materials for risk assessment and permits better prenatally counseling and preparation of parents facing the birth of isochromosome Y fetuses.

目的 探讨二代测序(NGS)技术在常染色体隐性遗传性多囊肾病(ARPKD)家系胚胎植入前遗传学检测(PGT)中的应用价值.方法 选取1个ARPKD家系,采用Sanger测序调查家系成员多囊肾/多囊肝病变1(PKHD1)基因突变情况.以PKHD1基因编码区为目标区域,在基因上下游2 M区域内选择120个高密度紧密连锁的单核苷酸多态性(SNP)位点作为遗传连锁标记,采用多重聚合酶链反应(PCR)和NGS选择有效SNP位点构建家系成员的SNP单倍型,确定夫妇双方携带基因突变的风险染色体.对活检获得的滋养层细胞进行全基因组扩增,采用NGS对胚胎的PKHD1基因突变位点进行直接测序,构建胚胎SNP单倍型进行连锁分析.采用Sanger测序验证胚胎PKHD1基因突变位点NGS结果.对正常和携带杂合突变的胚胎进行低深度的染色体非整倍性筛查.结果 家系成员中,父亲携带PKHD1基因c.5935G>A,为杂合子;母亲携带PKHD1基因c.10058T>G,为杂合子;先证者携带PKHD1基因c.5935G>A和c.10058T>G双重杂合突变.用于活检的5个胚胎中有2个未检测到突变,有3个携带杂合突变.低深度的染色体非整倍性筛查显示5个胚胎中3个为整倍体,2个为非整倍体.选择未检测到突变且发育良好的整倍体胚胎植入母体子宫后,足月分娩一健康婴儿.结论 应用NGS对ARPKD家系进行PGT,可阻断此单基因病在该家系中的再发风险,同时还可避免选择非整倍体胚胎而导致的流产问题.

Abstract Objective We present a prenatal case of 45,X/46,dic(X) with two asymmetric chromosome arms. Methods Single nucleotide polymorphism array(SNP-array),fluorescence in situ hybridization(FISH) and conventional cytogenetic analysis were performed for verification. Results The conventional G-banding analysis revealed a mosaic karyotype of mos 45,X/46,X,dic (X;X) (p11.2;q10) and the C-banding analysis showed that the derivative X chromosome had two darkly stained bands near the centromere.Two green signals and single green signal (X chromosome cetromere) were observed simultaneously in the metaphases and interphases FISH confirmation test,which indicated a mosaicism for X chromosome in the uncultured amniocytes.The SNP-array results revealed two copy-number-loss on the X chromosome.One was a 54.3Mb deletion in Xp22.33-p11.22 including 414 genes.Another was a mosaic deletion in Xp11.22-q28. Conclusion A combination of molecular and cytogenetic techniques should be employed to provide adequate genetic counseling to mosaic Turner sydrome patients for avoiding misdiagnosis.

目的 探讨14q32微缺失综合征的临床表现,进一步提高对该疾病的认识及对该疾病的产前及遗传学诊断.方法 对1例因"出生后口吐白沫伴气促1天"入院的胎儿进行遗传学诊断,结合常规染色体G显带分析及单核苷酸多态性微阵列(single nucleotide polymorphism array,SNP-array)技术进行分子细胞遗传学检测,并进行全基因组拷贝数变异分析.结果 发现14号染色体14q32.2-q32.31位置发生缺失,片段大小约5.83Mb,包含128个基因.结论 14q32印迹区域缺失可表现有"UPD(14)综合征"类似的临床症状,表现为Temple综合征或Kagami-Ogata综合征.

目的:探讨8p倒位重复[inv dup (8p)]染色体重排的临床表现及分子机制。方法:对3例产前超声发现异常的胎儿进行染色体G显带及染色体微阵列分析，并结合相关文献对inv dup(8p)的产前临床表现及相关基因进行总结。结果:3例胎儿产前超声均提示为心脏结构异常；染色体核型及染色体微阵列分析结果提示均为inv dup(8p)，倒位重复涉及的断裂位点不一，该区域包含 GATA4、 SOX7、 NRG1等基因。 结论:inv dup(8p)的主要表型为心脏及中枢神经系统异常；8p区域涉及的 GATA4、 SOX7基因与inv dup(8p)胎儿心脏异常相关。本研究3例inv dup(8p)染色体重排可能由染色体U交换机制导致。

Genomic disorders caused by pathogenic copy number variation (pCNV) have proven to underlie a significant proportion of birth defects. With technological advance, improvement of bioinformatics analysis procedure, and accumulation of clinical data, non-invasive prenatal screening of pCNV (NIPS-pCNV) by high-throughput sequencing of maternal plasma cell-free DNA has been put to use in clinical settings. Specialized standards for clinical application of NIPS-pCNV are required. Based on the discussion, 10 pCNV-associated diseases with well-defined conditions and 5 common chromosomal aneuploidy syndromes are recommended as the target of screening in this consensus.Meanwhile, a standardized procedure for NIPS-pCNV is also provided, which may facilitate propagation of this technique in clinical settings.

Background: Complex chromosome rearrangement (CCR) is a structural rearrangement involving more than two breakpoints. CCR carriers are at high risk for phenotypic abnormalities or reproductive failure, such as chromosomal abnormalities in fetuses and infertility.Methods: We presented a carriers with chromosome (3,18) apparent balanced translocation diagnosed in eleswhere, whose fetus had duplications in chromosome 3 and deletions in chromosome 10 demonstrated by chromosome microarray analysis(CMA). Results: Through the high resolution of GTG-banding, a cryptical translocation in chromosome 10 was found and the karyotype of the carrier was revised as 46,XY,t(3;10;18) (p26.3;q26.1;q21.1).In the cycle of preimplantation genetic diagnosis (PGD),21 oocytes were retrieved, and 15 were fertilized. At last 7 embryos were biospied and sent to diagnosis by next generation sequencing(NGS).Unfortunately, none of the NGS results from the 7 biopsy embryos were normal. Combining previous literature and our results, we assessed the odds of a balanced embryo in a CCR carrier to be about 9.3%(28/302).The transferable embryo rate was approximately 71.4%(20/28) and healthy live born delivery rate was 55%(11/20).Conclusions: NGS and CMA featured high automation, relatively low cost, high throughput, and high repeatability, which made them commonly used during prenatal diagnosis and PGD. The multiple technology combination can provide more accurate diagnosis and better fertility services for CCR patients.

目的 探讨二代测序(NGS)在Meckel综合征植入前遗传学检测(PGT)的应用价值和优势.方法 选取1例Meckel综合征家系,通过Sanger测序调查家系成员MKS1基因突变情况.以MKS1基因编码区为目标区域,在该基因上下游2M区域内选择200个单核苷酸多态位点(SNP)作为遗传连锁标记,多重PCR和NGS后选择有效SNP位点构建家系成员SNP单倍型,确定携带MKS1基因突变的风险染色体.采用NGS对胚胎MKS1基因突变位点直接测序和构建胚胎SNP单倍型进行PGT.对未检测到突变和杂合携带的胚胎进行了低深度的染色体非整倍性筛查.结果 采用NGS对胚胎基因突变位点直接测序和构建SNP单倍型结果显示活检的6个胚胎中3个未检测到突变,2个杂合携带,1个致病.5个未检测到突变和杂合携带胚胎染色体非整倍体筛查结果显示其中4个为平衡的整倍体胚胎.结论 应用NGS对Meckel综合征家系进行PGT,可以阻断此单基因病在该家系中的再发风险,还可以避免选择非整倍体胚胎而导致的流产问题.

Abstract Objective To determine the best method for chromosome detection of mosaicism by comparing the results of karyotype and SNP-array in amniotic fluid,chorionic villi and cord blood. Methods A total of 14,805 pregnant women underwent invasive prenatal diagnosis.SNP-array and karyotype analysis were used to detect chromosomal abnormalities. Results A total of 169 cases of mosaicism were detected in this study.Mosaicism was found in both karyotype and SNP-array in 99(0.66%,99/14,805) cases of prenatal samples. In the remaining 70 cases of mosaicism, the results of karyotype and SNP-array were discrepant with ten cases(1.04%,10/959),forty-five cases (0.5%,45/9034) and fifteen cases(0.31%,15/4812) dectected from CV,AF and CB respectively. The mosaic positive rate of karyotype analysis only was 1.11%(164/14,805), which was significantly higher than that of SNP-array (0.7%,104/14,805), and the difference was statistically significant (P < 0.001). The mosaic positive rate of combination with SNP-array and karyotype was 1.14%(169/14,805), which was higher than that of SNP-array(0.7%). Conclusions This study demonstrated that the combination of SNP-array and karyotype analysis may be the best strategy for the prenatal diagnosis of mosaicism aneuploidy.These two techniques have their own advantages and disadvantages, which can complement each other in clinical application.

Objective To explore the application value of next generation sequencing (NGS) in preimplantation genetic diagnosis of α/β complex thalassemia couple. Methods The coding regions of α-globin genes (HBA1, HBA2) and β-globin gene (HBB) were selected as the target regions. The high-density and closely linked single nucleotide polymorphism (SNP) sites were selected as the genetic linkage markers in the upstream and downstream 2M regions of the gene. After NGS, the effective SNP sites were selected to construct the haplotype of the couple, and the risk chromosome of the mutation carried by the couple was determined. The NGS technology was used to sequence the variations of HBA1, HBA2 and HBB directly and construct haplotype linkage analysis for preimplantation genetic diagnosis. Results Direct sequencing and haplotype linkage analysis of HBA1, HBA2 and HBB showed that two of the six blastocysts were α/β complex thalassemia, one was β-thalassemia heterozygote, two were α-thalassemias heterozygotes, and one was intermediate α-thalassemia. A well-developed embryo underwent preimplantation genetic diagnosis was implanted into the mother's uterus, and a healthy infant was born at term. Conclusion Preimplantation genetic diagnosis can be carried out by NGS technology in α/β complex thalassemia couples, and abortion caused by aneuploid embryo selection can be avoided.

目的 报道应用基于高通量测序的植入前遗传学检测(preimplantation genetic testing,PGT)技术对1例染色体平衡易位家系的胚胎染色体进行分析,探讨了染色体平衡易位夫妇的胚胎整倍体率和形成机制.方法 应用体外受精(in vitro fertilization,IVF)、囊胚培养和基于高通量测序的PGT技术对胚胎染色体进行分析,统计染色体平衡易位夫妇的胚胎整倍体率.结果 经卵胞浆内单精子注射(intracytoplasmic sperm injection,ICSI)技术受精,获得囊胚15个,活检10个.依据Garnder囊胚分级法分级,1号胚胎为B/4ab,2～7号胚胎为B/4bb,8～9号胚胎为B/6bb,10号胚胎为B/5bc.高通量测序数据提示:6枚整倍体囊胚,4枚非整倍体囊胚.女方最终移植1枚B/4bb整倍体囊胚,足月顺产1男婴,体重3.41kg,发育正常.结论 基于高通量测序的PGT技术可准确筛查出染色体整倍体胚胎,有效避免因胚胎染色体异常而导致的流产和出生缺陷.

Objective:To investigate the prenatal genetic testing for suspected Beckwith-Wiedemann syndrome (BWS) to improve its prenatal diagnosis rate.Methods:This study reported a pregnant woman, who had a pregnant history of termination due to the same reason at 18 weeks, with fetal acromphalus and unusually thickened placenta indicated by ultrasound examination at 13 weeks of gestation. After chorionic villus sampling, single nucleotide polymorphism (SNP) array was used to analyze copy number variations in the whole genome, and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) was also performed to detect the methylation and copy number variations in H19 and KCNQ1 genes on chromosome 11p15. Peripheral blood samples were collected from the couple for chromosome G-banding karyotype analysis and SNP array. Results:The SNP array indicated a 176 kb heterozygous deletion in the 11p15.5 region. MS-MLPA revealed a loss of methylation at imprinting control region 2 and a 50% reduction of copy numbers of KCNQ1 (L02903) gene. No abnormality was found in the parents in the SNP array and G-banding karyotype analysis. The fetus was prenatally diagnosed with BWS. Conclusions:When intrauterine abnormalities, such as acromphalus and abnormal thickening of the placenta, are found by ultrasound during early pregnancy, prenatal genetic tests related to BWS, including MS-MLPA and SNP array, are suggested to avoid a missed diagnosis of BWS.

Objective:To evaluate the detection of copy number variation (CNV) by chromosome microarray analysis (CMA) in fetuses with congenital anomalies of the kidney and urinary tract (CAKUT).Methods:A total of 1 929 fetuses who were ultrasonically found with CAKUT and underwent CMA from Guangdong Women and Children's Hospital and Health Institute were enrolled in this retrospective study from January 2016 to July 2020. These fetuses were divided into isolated CAKUT group ( n=1 567), CAKUT with soft markers group ( n=269), and CAKUT with other structural anomalies group ( n=93) for comparing the detection rate of pathogenic CNV using Chi-square test or Fisher exact test. Results:(1)The detection rate of all and pathogenic CNVs were 6.5%(125/1 929) and 4.8%(93/1 929), respectively. The total detection rate of CNV, clinically significant CNV and large chromosome structural variations in the CAKUT with other structural anomalies group were higher than those of the CAKUT with soft markers group and isolated CAKUT groups[31.2%(29/93), 11.5%(31/269) vs 4.2%(65/1 567), χ2=119.002; 18.3%(17/93), 9.0%(24/269) vs 3.6%(56/1 567), χ2=49.677; 9.7%(9/93), 2.2%(6/269) vs 0.3%(4/1 567), χ2=42.727; all P<0.001]. CAKUT with other structural anomalies group had a higher detection rate of pathogenic CNV (18.3%, 17/93) than the CAKUT with soft markers group (8.6%, 23/269) and the isolated CAKUT group [3.4%(53/1 567)] ( χ2=51.932, P<0.001). (2) The detection rate of pathogenic CNV was the highest in fetuses with enhanced renal echo (14.7%, 23/156), followed by renal enlargement (8.2%, 5/61), renal dysplasia (5.0%,13/261), polycystic renal dysplasia (5.0%, 13/261), and hydronephrosis (4.8%, 20/413). Fetuses with polycystic renal dysplasia, renal agenesis, fused kidney and hydronephrosis in the CAKUT with other structural anomalies group had a higher detection rate of pathogenic CNV than those in the isolated CAKUT group [3/9 vs 3.5%(8/230), 2/17 vs 1.3%(3/237), 1/8 vs 0.0%(0/59) and 3/18 vs 3.4%(12/344), all P<0.017]. The CAKUT with other structural anomalies group had a higher detection rate of pathogenic CNV than CAKUT with soft markers group in fetuses with enhanced renal echo [4/8 vs 12.8%(5/39), P<0.017]. (3) The top three microdeletion/microduplication syndrome were 17q12 microdeletion syndrome (36.6%, 34/93), 22q11.2 microdeletion syndrome (23.7%, 22/93), and 16p11.2 microdeletion syndrome (7.5%, 7/93) among those with pathogenic CNV. Conclusions:The risk of CNV in fetuses with isolated CAKUT, CAKUT with soft markers, and CAKUT with additional structural anomalies increased progressively. CMA might be a better choice in fetuses with hydronephrosis, enhanced renal echo, renal enlargement, renal hypoplasia, and multicystic renal dysplasia to improve the detection rate of CNV.