Role of echocardiography in assessing copy number variation in fetal congenital heart disease / 中华围产医学杂志

Objective:This study examines the application of echocardiography in the prenatal diagnosis of copy number variation (CNV) associated with fetal congenital heart disease (CHD).Methods:A retrospective analysis was conducted on 447 singleton pregnancies from Quanzhou Maternal and Child Care Hospital (Quanzhou Children's Hospital) from January 2019 to August 2022. These individuals underwent echocardiographic assessments suggestive of fetal CHD and subsequently received invasive prenatal diagnoses. Comprehensive karyotype analysis and chromosome microarray analysis (CMA) were performed for each case. The discrepancies in the chromosomal abnormality detection were analyzed between the results produced by CMA and karyotype analysis. Furthermore, differences in the detection of pathogenic copy number variation (pCNV) between the two methods in CHD cases with diverse cardiac phenotypes, including the presence or absence of extracardiac structural malformations, the type, and quantity of cardiac structural anomalies, were explored. Statistical analysis was conducted using the Chi-square test. Results:Compared with conventional karyotype analysis, CMA demonstrated a higher detection rate of fetal chromosomal abnormalities [10.5% (47/447) vs. 20.6% (92/447), χ 2=161.56, P<0.001]. In terms of distinct cardiac phenotypes, CHD cases with extracardiac structural anomalies displayed an escalated pCNV detection rate in comparison to isolated CHD cases [11.4% (45/394) vs. 32.1% (17/53), χ 2=16.68, P<0.001]. Within the cardiac structural anomaly subgroups, increased pCNV detection rates were observed in the septal defect subgroup, conotruncal malformation subgroup, and left ventricular malformation subgroup [18.4%(29/158), 25.9%(7/27), and 25.0%(7/28) vs. 7.6%(16/210); χ 2=9.15, 9.68, and 8.55, respectively, all P<0.05]. The CMA-identified pCNV correlated with CHD included 22q11.2 deletions/duplications in eight cases, 4p16.3 deletions in two cases, 11q23.3 microduplications in two cases, 1q21.1 microdeletions/microduplications in two cases, 4q28.3 microduplications in one case, and 10p15.3 microdeletions in one case. Conclusions:CMA technology exhibited an enhanced ability to detect pCNV in fetuses with CHD. Echocardiography can guide targeted CMA screening, thereby facilitating prenatal genetic assessment of CHD.

Analysis of cell mutation types of colorectal neuroendocrine tumors / 基础医学与临床

Objective To investigate the mutation types of colorectal neuroendocrine tumors(NETs)and better un-derstand the pathogenesis of colorectal nets.Methods Patients undergoing colorectal NETs surgery were recruited,colorectal NETs and corresponding adjacent cancerous tissues were collected,and whole genome sequencing(WGS)was performed and further deeply analyzed.Results WGS sequencing showed that the mutation types of colorectal NETs included single nucleotide mutations,insertion and deletion mutations(InDel,less than 50 bp in length),copy number variations(CNV),and large structural variations(SV,more than 50 bp in length),such as insertion(INS),deletion(DEL),intra chromosomal translocation(ITX),inter chromosomal translocation(CTX)and inversion(INV).Conclusions A large number of somatic mutations occur in colorectal NETs,especially chro-mosome translocation

Identification of a rare copy number polymorphic gain at 3q12.2 with candidate genes for familial endometriosis

Abstract Endometriosis is a complex disease that affects 10-15% of women of reproductive age. Familial studies show that relatives of affected patients have a higher risk of developing the disease, implicating a genetic role for this disorder. Little is known about the impact of germline genomic copy number variant (CNV) polymorphisms on the heredity of the disease. In this study, we describe a rare CNV identified in two sisters with familial endometriosis, which contain genes that may increase the susceptibility and progression of this disease. We investigated the presence of CNVs from the endometrium and blood of the sisters with endometriosis and normal endometrium of five women as controls without the disease using array-CGH through the Agilent 2x400K platform. We excluded common CNVs that were present in the database of genomic variation. We identified, in both sisters, a rare CNV gain affecting 113kb at band 3q12.2 involving two candidate genes: ADGRG7 and TFG. The CNV gain was validated by qPCR. ADGRG7 is located at 3q12.2 and encodes a G protein-coupled receptor influencing the NF-kappaβ pathway. TFG participates in chromosomal translocations associated with hematologic tumor and soft tissue sarcomas, and is also involved in the NF-kappa B pathway. The CNV gain in this family provides a new candidate genetic marker for future familial endometriosis studies. Additional longitudinal studies of affected families must confirm any associations between this rare CNV gain and genes involved in the NF-kappaβ pathway in predisposition to endometriosis.

DNA rare copy number alterations in Reinke's Edema

Abstract Introduction: Reinke's Edema (RE) is a laryngeal lesion related to excessive tobacco smoking, voice overuse, and laryngopharyngeal reflux. Although the risk of malignancy has been considered low in literature, RE is classified among precancerous lesions. Objectives: We investigated DNA Copy Number Alterations (CNAs) in specimens of RE and its potential association with malignant progression. Methods: We used array-based comparative genomic hybridization (aCGH, Agilent 4 × 180 K platform) to study eight RE cases. All patients were heavy tobacco users for at least 30 years, and none of them progressed to cancer in the follow-up (>8 years). Two RE presented mild dysplasia, one moderate dysplasia, and no histological alterations were found in the remaining five cases. CNAs were compared with the Database of Genomic Variants (DGV) and genes mapped on altered regions had their functions annotated. Results: Six of eight patients showed different rare copy number alterations on chromosomes 2q37.3, 4q13.1, 4q13.3, 7q11.22, 10p14, and 13q34. A gain of the whole chromosome 8 were detected in one case. Of interest, four of eight RE cases showed copy number imbalances involving genes previously described in several tumor types (RASA3, COL6A3, LINC00707, LINP1, SMR3A, and SMR3B). Conclusion: The genomic imbalances herein found in RE have the potential to contribute to the phenotype but with limited or no risk of cancer. A long-term follow-up in a large series of patients could clarify the mechanisms involved in the malignant progression of RE. Level of evidence: 4.

High diagnostic yield with algorithmic molecular approach on hereditary neuropathies

SUMMARY OBJECTIVE: Charcot-Marie-Tooth disease covers a group of inherited peripheral neuropathies. The aim of this study was to investigate the effect of targeted next-generation sequencing panels on the molecular diagnosis of Charcot-Marie-Tooth disease and its subtypes in routine clinical practice, and also to show the limitations and importance of next-generation sequencing in the diagnosis of Charcot-Marie-Tooth diseases. METHODS: This is a retrospective study. Three different molecular methods (multiplex ligation probe amplification, next-generation sequencing, and whole-exome sequencing) were used to detect the mutations related to Charcot-Marie-Tooth disease. RESULTS: In total, 64 patients (33 males and 31 females) with suspected Charcot-Marie-Tooth disease were analyzed for molecular etiology. In all, 25 (39%) patients were diagnosed by multiplex ligation probe amplification. With an extra 11 patients with normal PMP22 multiplex ligation probe amplification results that were consulted to our laboratory for further genetic analysis, a total of 50 patients underwent next-generation sequencing for targeted gene panels associated with Charcot-Marie-Tooth disease. Notably, 18 (36%) patients had pathogenic/likely pathogenic variants. Whole-exome sequencing was performed on five patients with normal next-generation sequencing results; the diagnostic yield by whole-exome sequencing was 80% and it was higher in the childhood group. CONCLUSION: The molecular etiology in Charcot-Marie-Tooth disease patients can be determined according to pre-test evaluation, deciding the inheritance type with pedigree analysis, the clinical phenotype, and an algorithm for the genetic analysis. The presence of patients without a molecular diagnosis in all the literature suggests that there are new genes or mechanisms waiting to be discovered in the etiology of Charcot-Marie-Tooth disease.

Prenatal diagnosis of Pallister-Killian syndrome: a report of two cases / 中华围产医学杂志

This article reported two fetuses diagnosed with Pallister-Killian syndrome (PKS). Amniotic fluid samples of one pregnant woman (case 1), with an abnormal result of non-invasive prenatal test, were analyzed by karyotyping and copy number variation-sequencing (CNV-seq), and samples of the other one (case 2), with a prenatal ultrasound of a lowered spinal conus and an enhanced echo of the renal cortex, were tested for CNV-seq. The chromosome karyotype of case 1 showed 47,XN,+mar[30]/46, XN[10]. CNV-seq results revealed three to four copies of repetition of the p13.33p11.1 segment of chromosome 12, suggesting 12p tetrasomy chimerism in both fetuses. The diagnosis of fetal PKS was confirmed through the combination of multiple technologies (ultrasound, chromosomal karyotype analysis, and CNV-seq). The two pregnancies were terminated after genetic counseling.

Prenatal diagnosis and genetic counseling of 1q21.1 distal microdeletion/microduplication in 14 fetuses / 中华围产医学杂志

Objective:To explore the clinical phenotypes, pregnancy outcomes, and follow-up of fetuses with 1q21.1 distal microdeletion/microduplication, and to provide a basis for prenatal and genetic counseling.Methods:This was a retrospective study involving 14 singleton fetuses with 1q21.1 distal microdeletion/microduplication that were prenatally diagnosed by karyotype analysis and chromosomal microarray analysis (CMA) at Wuxi Maternity and Child Health Care Hospital from January 2017 to June 2022. The results of ultrasound and genetic analysis, pregnancy outcome after genetic counseling, and postnatal follow-up were summarized using descriptive statistical methods.Results:All 14 fetuses had normal karyotypes. Out of the 14 cases, CMA indicated 1q21.1 distal microdeletion in eight cases and 1q21.1 distal microduplication in six cases. The fragments ranged from 813 kb to 4.48 Mb, all of which contained the key region of 1q21.1 microdeletion/microduplication syndrome and were pathogenic copy number variations (CNV). Among eight fetuses with distal 1q21.1 microdeletion, four cases had abnormal prenatal ultrasound findings, including one case with overlapping fingers of left hand and polyhydramnios, two were small for gestational age, and one with small head circumference. Among the six cases who underwent parental origin detection, the microdeletions were de novo in four fetuses and two fetuses were inherited from the parent with normal phenotype. As for six fetuses with distal 1q21.1 microduplication, nasal bone absence or hypoplasia was shown by ultrasound in four cases and no obvious abnormality was found in the other two cases. Parental origin detection was performed in four cases, which found that one case was de novo and the other three cases were inherited from their phenotypically normal parents. After genetic counseling, five families chose to terminate the pregnancies and the remaining nine cases continued the pregnancies to delivery. The last follow-up showed that all of the nine live births grew well, whose ages ranged from seven months to half past five years old. Conclusions:CMA is of great value in prenatal diagnosis of 1q21.1 distal microdeletion/ microduplication. Ones carrying pathogenic CNV may not develop the disease. Combined with ultrasound findings and parental genetic tracing results, individualized genetic counseling and long-term follow-up are of great importance for reasonable guidance in pregnancy outcome and reproduction.

Atrial septal defect and hydronephrosis associated with 2q13 microdeletion: a case report and literature review / 中华围产医学杂志

Objective:To investigate the clinical and genetic features of 2q13 microdeletion.Methods:This study retrospectively analyzed the clinical and genetic features and prognosis of an infant who was admitted to the Fourth People's Hospital of Zhenjiang Affiliated to Jiangsu University and diagnosed with 2q13 microdeletion in October 2021. A literature review on the clinical and genetic characteristics of 2q13 microdeletion was conducted by searching CNKI, Wanfang database, Yiigle, VIP database, PubMed, Embase, and Cochrane Library databases up to March 2023, with "2q13 microdeletion" and "2q13" (both in Chinese and English) as the keywords.Results:(1) Case report: A fetus was found to have mild aortic arch stenosis and left hydronephrosis by prenatal ultrasound at 24 +2 gestational weeks. Fetal chromosomal microarray analysis following amniocentesis at 27 +6 weeks of gestation revealed a 2.23 Mb deletion at 2q13q14.1 chromosome, considered a possible pathogenic copy number variation. The newborn was delivered by cesarean section at 38 +5 weeks of gestation. Echocardiography indicated ostium secundum atrial septal defect and ultrasound showed left hydronephrosis. Other examinations detected no abnormalities. Results of imaging reexamination showed no significant changes when followed up by telephone at 13 months after birth, and a continued follow-up was recommended by the pediatrician. No other developmental abnormalities were found. (2) Literature review: There were 64 patients in 32 retrieved literature, and the one case in this report results in 65 cases. The 2q13 microdeletions can be de novo (15.6%, 10/64) or inherited from one of the parents with normal or abnormal phenotypes (35.9%, 23/64). The clinical manifestations include developmental delay (53.3%, 16/30), craniofacial abnormalities (56.8%, 21/37), and congenital heart diseases (35.0%, 14/40). In addition, some cases exhibited mental neurological symptoms with age, such as attention deficit hyperactivity disorder (48.0%, 12/25), autism spectrum disorders (35.7%, 10/28), etc. Conclusions:The 2q13 microdeletion is complex in its clinical characteristics and incomplete in penetrance. Chromosomal microarray analysis is recommended for confirming diagnosis when related phenotypes are identified prenatally. Some cases of 2q13 microdeletion will show neuropsychiatric symptoms with age, suggesting that long-term follow-up is necessary.

Detection of meningeal carcinomatosis by metagenomic next-generation sequencing and copy number variation analysis of cerebrospinal fluid / 中华神经科杂志

Objective:To evaluate the significance of copy number variation (CNV) and metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) in the diagnosis of meningeal carcinomatosis (MC).Methods:Ten patients with MC diagnosed in the Department of Neurology of Peking Union Medical College Hospital from March 2022 to June 2022 were consecutively enrolled in this study. The patients were diagnosed according to the criteria of the Chinese expert consensus on the diagnosis of MC by the Chinese Society of Infectious Diseases and Cerebrospinal Fluid Cytology, and the diagnosis of MC was confirmed by CSF cytology. The control group included 10 patients who were diagnosed as autoimmune encephalitis or viral encephalitis. CSF mNGS and CNV analysis were performed simultaneously in all the patients.Results:Of the 10 patients with MC, 6 had lung adenocarcinoma, 4 had breast cancer. CSF mNGS and CNV analysis detected large CNV in 8 of 10 patients with MC, including 4 patients with breast cancer and 4 patients with lung cancer. The results of pathogenic microorganism analysis of CSF mNGS in all the patients were negative. Meanwhile, large CNV was not detected in the control group.Conclusions:CSF CNV can serve as a diagnostic marker for MC. The combination of mNGS and CNV analysis has demonstrated a high positive rate in the diagnosis of MC. The dual-omics analysis of pathogenic microorganisms and CNV has been proposed as a potential strategy to further expand the clinical utility of CSF mNGS in the realm of auxiliary diagnosis.

Copy number variation analysis and outcomes of 1 658 fetuses with increased nuchal translucency / 中华围产医学杂志

Objective:To analyze the genetic etiology and prognosis in fetuses with increased nuchal translucency (NT) in order to assist in the clinical prenatal genetic counseling and diagnosis.Methods:This study retrospectively enrolled 1 658 cases of singleton pregnancy (<35 years old) receiving invasive prenatal diagnosis, including karyotype analysis and/or chromosome microarray analysis or copy number variation (CNV) sequencing, due to NT value ≥2.5 mm in the first trimester in Henan Provincial People's Hospital from August 2014 to December 2021. They were divided into different groups according to the thickness of NT (≥2.5-<3.0, ≥3.0-<3.5, ≥3.5-<4.5, ≥4.5-<5.5, ≥5.5-<6.5 and ≥6.5 mm groups) and abnormal ultrasound findings (isolated increased NT group, increased NT complicated by soft markers/non-severe structural abnormality group and increased NT complicated by severe structural abnormality group). The results of invasive prenatal diagnosis and pregnancy outcomes were compared between different groups using Chi-square test and trend Chi-square test. Results:The detection rates of numerical abnormalities of chromosomes were 15.8% (262/1 658) and 17.6% (252/1 431) when the NT thickness cut-off value were 2.5 mm or 3.0 mm, respectively. Overall, the detection rate of numerical abnormalities of chromosomes increased with thickness of NT ( χ2trend=180.75, P<0.001), ranging from 6.6% (44/671) in the NT≥2.5-<3.5 mm group to 45.6% (113/248) in the NT≥5.5 mm group. The incidence of pathogenic/likely pathogenic CNV(P/LP CNV) did not increased with NT thickness ( χ2trend=3.26, P=0.071), and the highest detection rate was observed in the NT≥4.5-<5.5 mm group (9.0%, 19/211). The detection rate of numerical abnormalities of chromosomes plus P/LP CNV in the isolated NT≥2.5-<3.0 mm group and NT≥3.0-<3.5 mm group were 5.3% (10/188) and 9.6% (36/375), respectively, however, the difference was not statistically significant ( χ2=3.06, P=0.080). The detection rates of numerical abnormalities of chromosomes plus P/LP CNV in the isolated NT≥3.5-<4.5 mm group and NT≥2.5-<3.0 mm complicated by soft markers/ non-severe structural abnormality group were 12.7% (52/410) and 24.1% (7/29), respectively, and the risk were 2.6 times (95% CI: 1.3-5.2) and 5.7 times (95% CI: 2.0-16.4) of the isolated NT≥2.5-<3.0 mm group, respectively. The pregnancy termination rate increased with the NT thickness ( χ2trend=304.42, P<0.001), ranging from 10.8% (23/212) in the NT≥2.5-<3.0 mm group to 90.7% (117/129) in the NT≥6.5 mm group. After exclusion of the pregnancies terminated due to numerical abnormalities of chromosomes and P/LP CNV, 87.6% (862/984) of the fetus with increased NT were born alive. Conclusions:The detection rate of numerical abnormalities of chromosomes increases with the thickness of NT. Invasive prenatal diagnosis is required for non-advance aged singleton pregnant women when fetuses present with isolated NT≥2.5 mm with or without soft markers/structural abnormalities.

Prenatal diagnosis and genetic analysis of seven fetuses with 16p12.2 microdeletion or microduplication / 中华围产医学杂志

Objective:To investigate the prenatal ultrasonographic features and diagnosis of 16p12.2 copy number variation (CNV).Methods:This retrospective study recruited seven fetuses with 16p12.2 microdeletion/microduplication in the First Affiliated Hospital of Fujian Medical University from January 2017 to December 2021. Data, including the prenatal diagnostic indications, ultrasound findings, karyotypes, genetic testing and mutation tracing results, pregnancy outcomes, and postnatal follow-up data, were summarized with descriptive statistical analysis.Results:Prenatal ultrasound indicated three fetuses with structural abnormalities, including one case each of multiple malformations, interventricular septal defect, and cleft lip and palate. The other four cases were positive for ultrasonic soft markers involving the heart and kidney. The chromosome karyotypes of the seven fetuses were normal. Single nucleotide polymorphism array (SNP array) results showed that four cases had a 381.7-542.4 kb microdeletion containing three genes ( OTOA, METTL9, and IGSF6) in Online Mendelian Inheritance in Man (OMIM) at 16p12.2 (distal region) and three cases had a 484.0-701.7 kb microdeletion/microduplication containing four OMIM genes ( UQCRC2, CDR2, EEF2K, and POLR3E) at 16p12.2 (proximal region). Five (cases 1, 2, 4, 5, and 6) out of the seven fetuses inherited the variants from their phenotypically normal mother/father, and among them, three (cases 2, 4, and 5) were delivered at term and healthy. Two cases (cases 3 and 7) refused to undergo pedigree verification. Case 3, a full-term infant, underwent ventricular septal defect repair three months after birth, and no abnormality was found at 18 months of age. Conclusions:No specific phenotype presents in fetuses with 16p12.2 microdeletion/microduplication in prenatal diagnosis. OTOA gene is the key gene associated with abnormality in the distal region of 16p12.2. Pedigree analysis is conducive to preventing unnecessary termination of pregnancy.

Genetic etiology of fetal conotruncal defects and significance of copy number variation sequencing and whole exome sequencing: analysis of 196 cases / 中华围产医学杂志

Objective:To investigate the genetic etiology of fetal conotruncal heart defects (CTDs) and to evaluate the performance of copy number variation sequencing (CNV-seq) and whole exome sequencing (WES) in identifying the genetic etiology.Methods:This retrospective study involved 196 fetuses diagnosed with CTDs by fetal echocardiography in Beijing Anzhen Hospital, Capital Medical University from June 2017 to December 2021. CNV-seq was performed to screen for chromosomal abnormalities [aneuploidy and copy number variations (CNVs)] in the fetuses and their parents, and then WES was performed if CNV-seq was negative. The diagnostic yields of genetic abnormalities [aneuploidy+CNVs+single nucleotide variations (SNVs)] for different types of CTDs were compared using Chi-square test. Results:CNV-seq revealed 54 cases (27.6%, 54/196) with chromosomal abnormalities, including 14 (7.1%, 14/196) aneuploidies, 39 (19.9%, 39/196) CNVs and one aneuploidy complicated by CNVs. Together with another 13 fetuses with pathogenic or likely pathogenic SNVs detected by WES among the rest 142 cases whose CNV-seq results were negative, the total detection rate of genetic abnormalities was 34.2% (67/196). WES increased the diagnostic yield for CTDs by 9.2% (13/142). There was significant difference in the diagnostic yields for different types of CTDs ( χ2=20.31, P=0.002). The diagnostic yield was relatively high for interrupted aortic arch of type B, absent of the pulmonary valve -type of tetralogy of Fallot (9/10 and 8/12), but low for transposition of the great arteries (12.5%, 5/40). Conclusions:CNVs are the common genetic abnormalities in fetal CTDs, and SNVs are also detected in some cases. It is recommended that all fetuses with CTDs should undergo genetic testing. CNV-seq should be used in combination with WES if possible to improve the identification of genetic etiology and provide reference for genetic counseling.

Application value of low depth and high-throughput gene sequencing to detect chromosome copy number variations in prenatal diagnosis / 中国医师杂志

Objective:To explore the application value of low depth and high-throughput gene sequencing in detecting chromosome copy number variations (CNVs) in different risk indicators of prenatal diagnosis.Methods:We retrospectively analyzed the genetic testing results of 1 597 pregnant women who underwent amniocentesis in Maternal and Child Health Care of Zaozhuang from January 2017 to December 2020 to obtain amniotic fluid cells and undergo high-throughput gene sequencing for chromosome copy number variation (CNV-seq). The CNV-seq results was compared with G-banding karyotype analysis.Results:The success rate of CNV-seq detection in 1 597 cases of amniotic fluid cells was 100%, and 301 cases of chromosomal CNVs were found, with an abnormal rate of 18.85%. Among them, 208 cases of chromosomal CNVs with definite pathogenicity accounted for 69.10%; There were 93 cases of CNVs with unknown pathogenicity, accounting for 30.90%. Among 208 cases of CNVs with definite pathogenicity, 166 cases had abnormal chromosome aneuploidy, accounting for 79.81%; 42 cases of chromosomal deletion / duplication structural abnormality, accounting for 20.19%. The detection of chromosomal copy number abnormalities in different prenatal diagnosis indicators was different. The incidence of chromosomal CNVs in the NIPT screening risk group was the highest (53.09%, 163/307), followed by the ultrasonic structural abnormality group (22.38%, 32/143), the chromosomal abnormality carrying group (12.50%, 5/40), the other abnormality group (11.34%, 22/194), the serological prenatal screening high-risk group (9.04%, 74/819), and the elderly group (5.32%, 5/94). Compared with G-banding karyotype analysis, CNV-seq has a detection rate of 100% for 166 cases of chromosomal aneuploidy and 13 cases of unbalanced chromosomal structural abnormalities confirmed by G-banding karyotype analysis. In addition, and more pathogenicity specific chromosomal microdeletions / microduplication abnormalities can be found by CNV-seq.Conclusions:CNV-seq has high success rate and short time-consuming in the detection of chromosome CNVs, which can effectively avoid the failure of karyotype analysis and the problem of time-consuming; Moreover, CNV-seq can also find additional CNVs with clear pathogenicity, improve the positive detection rate, and effectively prevent the birth of defective children. Therefore, pregnant women with different prenatal diagnosis indications should be tested with CNV-seq at the same time of amniotic fluid karyotype analysis. CNV-seq can be used as a first-line auxiliary diagnostic technology in prenatal diagnosis for clinical application.

Genetic analysis of 387 cases of fetal sex chromosome abnormalities detected from amniotic fluid samples / 中华围产医学杂志

Objective:To analyze fetal sex chromosome abnormalities in prenatal diagnosis based on amniotic fluid cell culture.Methods:Clinical data of 12 164 pregnant women who underwent amniocentesis in Maternal and Child Health Hospital of Hunan Province from January 2017 to December 2020 were retrospectively analyzed. For those diagnosed with fetal sex chromosome abnormalities, the results of karyotyping and chromosome microarray analysis (CMA) were analyzed and described.Results:(1) Among the 12 164 cases, fetal sex chromosome abnormalities were detected in 387 cases (3.2%), including 351 cases with abnormal sex chromosome karyotype and 36 with sex chromosome microdeletion/microduplication. (2) High-risk patients indicated by non-invasive prenatal test (NIPT) had the highest proportion of sex chromosomes abnormalities (74.2%, 287/387), followed by those with other ultrasound abnormalities (8.5%, 33/387), high risk of Down syndrome screening (7.0%, 27/387), advanced maternal age (4.7%, 18/387), history of adverse pregnant or delivery (3.3%, 13/387), and nuchal translucency thickening or cervical lymphatic hygroma (2.3%, 9/387). (3) Detected chromosome karyotype abnormalities included numerical abnormalities [73.2%(257/351)], mosaicism [18.8(66/351)], and structural abnormalities [8.0%(28/351)], among which, 47,XXY [46.7%(120/257)], 45,X/46,XX[48.5%(32/66)], and X chromosome deletion [39.3%(11/28)] were the most common, respectively. Among 36 sex chromosome microdeletions/microduplications cases, 15(41.7%) were with pathogenic copy number variation (CNV), including 14 cases of X chromosome microdeletion/microduplication; 7(19.4%) with benign CNV, and 14(38.9%) with CNV of unknown clinical significance. The fragment size [ M (min-max)] of the 15 pathogenic CNV was 1.68 Mb(0.37-9.20 Mb). Of the nine cases with microdeletions, seven were found with deletion in the Xp22.31 region. Conclusions:Numerical abnormalities are the most common fetal sex chromosome abnormalities detected from amniotic fluid samples. Others included mosaicism and chromosome structure abnormalities.

Allosteric inhibition reveals SHP2-mediated tumor immunosuppression in colon cancer by single-cell transcriptomics

Colorectal cancer (CRC), a malignant tumor worldwide consists of microsatellite instability (MSI) and stable (MSS) phenotypes. Although SHP2 is a hopeful target for cancer therapy, its relationship with innate immunosuppression remains elusive. To address that, single-cell RNA sequencing was performed to explore the role of SHP2 in all cell types of tumor microenvironment (TME) from murine MC38 xenografts. Intratumoral cells were found to be functionally heterogeneous and responded significantly to SHP099, a SHP2 allosteric inhibitor. The malignant evolution of tumor cells was remarkably arrested by SHP099. Mechanistically, STING-TBK1-IRF3-mediated type I interferon signaling was highly activated by SHP099 in infiltrated myeloid cells. Notably, CRC patients with MSS phenotype exhibited greater macrophage infiltration and more potent SHP2 phosphorylation in CD68+ macrophages than MSI-high phenotypes, suggesting the potential role of macrophagic SHP2 in TME. Collectively, our data reveals a mechanism of innate immunosuppression mediated by SHP2, suggesting that SHP2 is a promising target for colon cancer immunotherapy.

Prenatal diagnosis and genetic analysis of 9p24 microdeletion in six fetuses / 中华围产医学杂志

Objective:To investigate the prenatal diagnosis and genetic analysis of 9p24 microdeletion in six fetuses.Methods:Genetic data of six pregnant women with positive results of serological Down's syndrome screening at Henan Provincial People's Hospital from January 2018 to January 2020 were retrospectively collected and analyzed. Amniotic fluid and the parents' peripheral blood samples were subjected to G banding and array comparative genomic hybridization (aCGH) analysis. Detected copy number variation (CNV) were classified based on the American College of Medical Genetics and Genomics (ACMG) scoring standard.Results:Six fetuses showed no abnormalities in ultrasound during the second trimester as well as in karyotyping. A chromosome deletion of 1 019~6 001 kb at 9p24 was found in all six fetuses by aCGH, referring to disease-related genes DMRT1, SMARCA2, DOCK8, etc. The deletion of case 3 was inherited from the asymptomatic father, and the other fetal five were all de novo mutations. Cases 1, 2, 5, and 6 were pathogenic/likely pathogenic CNV carriers and cases 3 and 4 were CNV of unknown clinical significance carriers. After genetic counseling, cases 1, 2, 5, and 6 chose to terminate the pregnancies; cases 3 and 4 continued and gave birth to normal offspring. Conclusions:Fetuses with 9p24 microdeletion lack specific phenotypes before born. DMRT1 and SMARCA2 may be the key genes in this region.

Copy number variant sequencing for chromosome analysis in 487 fetuses with increased nuchal translucency / 中华围产医学杂志

Objective:To analyze the genetic etiology of 487 fetuses with increased nuchal translucency (NT) using copy number variant sequencing (CNV-seq) and explore the relationship between increased NT and chromosomal abnormality.Methods:A retrospective study was performed on 487 fetuses with increased NT who received CNV-seq in the First Affiliated Hospital of Zhengzhou University from January 2018 to December 2020. These fetuses either had NT of ≥3.0-<3.5 mm (Group A, n=129) or ≥3.5 mm (Group B, n=358), the distribution and incidence of chromosomal abnormalities in the two sets of fetuses were analyzed using Chi square test or Fisher's exact test. Results:Fetuses with abnormal chromosomes accounted for 25.9%(126/487) of cases, including 107 with chromosome aneuploidy (22.0%) and 19 with pathogenic or likely pathogenic copy number variation (CNV, 3.9%). The detection rate of fetal aneuploidy in Group B was higher than that in Group A [14.0% (18/129) vs 24.9% (89/358), χ2=6.58, P=0.010]. However, no significant difference was observed regarding the detection rate of pathogenic or likely pathogenic CNV between the two groups ( χ2=0.30, P=0.584). Conclusions:The risk of fetal chromosome aneuploidy increased with NT thickness, but not with pathogenic or likely pathogenic CNV, which needed further verification due to the small sample size. CNV-seq is an option to detect the conventional detection methods for the genetic etiology of NT thickening fetuses.

Influence of copy number variations in the FCGR3A and FCGR3B genes on the outcome of hepatitis B virus infection / 临床肝胆病杂志

Objective To investigate the association of copy number variations (CNVs) in the FCGR3A and FCGR3B genes with different outcomes and disease progression after hepatitis B virus (HBV) infection. Methods Peripheral blood samples were collected from 841 patients with chronic HBV infection and 296 patients with self-limited HBV infection, an according to the degree of disease progression, the patients with chronic HBV infection were further divided into chronic hepatitis B (CHB) group, liver cirrhosis (LC) group, and hepatocellular carcinoma (HCC) group. The AccuCopy technique was used for the quantitative analysis of CNVs in the FCGR3A and FCGR3B genes in peripheral blood. The independent samples t -test was used for comparison of continuous data between two groups, and a one-way analysis of variance and the Kruskal-Wallis H test were used for comparison between multiple groups; the chi-square test was used for comparison of categorical data between groups. The chi-square test was also used to investigate the difference in the distribution of CNVs in the FCGR3 gene between different groups. The age-and sex-adjusted logistic regression model was used to investigate the influence of CNVs on the chronicity of HBV infection. Results There was a significant difference in the frequency distribution of CNVs in the FCGR3A and FCGR3B genes between the chronic HBV infection group and the self-limited HBV infection group ( χ 2 =11.406 and 19.143, both P < 0.05). As for disease progression after chronic HBV infection, there were no significant differences in CNVs of the FCGR3A and FCGR3B genes between the CHB group, the LC group, and the HCC group (FCGR3A: χ 2 =3.125, P =0.537; FCGR3B: χ 2 =5.274, P =0.260). There were also no significant differences in CNVs of the FCGR3A and FCGR3B genes between the HBeAg-positive group and the HBeAg-negative group (FCGR3A: χ 2 =1.025, P =0.599; FCGR3B: χ 2 =0.712, P =0.701). Reduction or deletion of the copy number of the FCGR3A and FCGR3B genes was a risk factor for the chronicity of HBV infection (FCGR3A: odds ratio [ OR ]=0.621, 95% confidence interval [ CI ]: 0.513-0.752; FCGR3B: OR =0.594, 95% CI : 0.491-0.719). Conclusion Reduction or deletion of the copy number of the FCGR3A and FCGR3B genes may be a genetic susceptibility factor for the chronicity of HBV infection, but it is not associated with disease progression.

Importancia de la determinación de variantes en el número de copias en neonatos con aneuploidías autosómicas / Importance of determining variations in the number of copies in newborns with autosomal aneuploidies

Resumen | Introducción. Las aneuploidías son trastornos genéticos frecuentes en la práctica clínica; sin embargo, se conoce poco sobre las otras variantes genéticas que modifican el fenotipo final. Objetivo. Determinar las variantes en el número de copias y las regiones con pérdida de heterocigosidad autosómica mayor de 0,5 % o de regiones mayores de 10 Mb en neonatos con aneuploidías autosómicas. Materiales y métodos. Se hizo el análisis cromosómico por micromatrices a los neonatos con aneuploidías autosómicas (n=7), trisomía 21 (n=5) y trisomía 18 (n=2) evaluados en los hospitales Antonio Lorena y Regional de Cusco, Perú, en el 2018. Resultados. En dos neonatos se encontraron variantes en el número de copias, patogénicas o probablemente patogénicas, en regiones diferentes al cromosoma 21 o al 18. Además, se observaron dos variantes del número de copias con más de 500 kpb de patogenia desconocida. Conclusiones. Si bien el número de pacientes era muy reducido, es importante resaltar que se encontraron otras variantes en el número de copias que se han descrito asociadas con trastornos del neurodesarrollo, varias anomalías congénitas, hipoacusia y talla baja o alta, entre otras, lo que probablemente influye negativamente en el fenotipo de este grupo de pacientes.

Abstract | Introduction: Aneuploidies are frequent genetic disorders in clinical practice. However, little is known about other genetic variants that may influence the final phenotype. Objective: To determine the variations in the number of copies and regions with homozygosity greater than 0.5% or larger than 10 Mb in newborns with autosomal aneuploidies. Materials and methods: We performed a chromosomal microarray analysis on newborns with autosomal aneuploidies (n=7), trisomy 21 (n=5), and trisomy 18 (n=2) evaluated at the Hospital Antonio Lorena and Hospital Regional of Cusco, Perú, during 2018. Results: We found pathogenic and probably pathogenic variants in the number of copies in other genomic regions different to chromosomes 21 or 18 in two neonates. Additionally, we found two variants bigger than 500 kpb of unknown pathogenicity. Conclusions: Although the number of analyzed individuals was small, it is important to highlight that we found other variants in the number of copies that have been described in association with neurodevelopmental disorders, congenital anomalies, deafness, and short/ tall stature, among others, in almost half of them, which will probably impact the phenotype negatively in patients with aneuploidies.

Application and clinical significance of TCGA molecular classification in endometrial cancer / 中华妇产科杂志

Objective:To explore the application and clinical significance of the cancer genome atlas (TCGA) molecular classification in endometrial cancer (EC).Methods:Sixty-six EC patients collected from December 2018 to March 2021 from Peking University People′s Hospital were categorized into four subgroups based on TCGA molecular classification tested by next generation sequencing. The correlation among four molecular subgroups and the clinical-pathological features including prognosis were analyzed.Results:(1) Clinical and pathological features: median age at diagnosis was 56 years (range: 24-78 years). The cases were distributed as follows: 3 (5%) cases DNA polymerase epsilon (POLE) ultra-mutated, 11 (17%) cases high microsatellite instability (MSI-H) including 2 Lynch syndrome, 42 (64%) cases low copy-number (CN-L) and 10 (15%) cases high copy-number (CN-H). There were significant differences among four subtypes in the combination of other tumors, tumor family history, surgical method, International Federation of Gynecology and Obstetrics (FIGO, 2009) stage, depth of muscle invasion and lymph vascular space invasion (all P<0.05). The proportions of patients in CN-H subgroup with advanced FIGO stage (stage Ⅲ-Ⅳ), deep muscle invasion and positive lymph-vascular space invasion were significantly increased. There were no significant differences in age, menopausal status, body mass index, metabolic syndrome-related complications, preoperative serum CA 125 and human epididymis protein 4 levels, tumor size, pathological grade (only endometrioid cancer), and lymph node metastasis among the 4 TCGA molecular types (all P>0.05). (2) Immuno-related molecular analysis: among 66 EC patients, 27 patients underwent immunohistochemical analysis of programmed cell death 1 ligand 1 (PD-L1) protein, and 28 patients underwent tumor mutation burden (TMB) detection. POLE and MSI-H subgroups contained TMB than those in CN-L and CN-H ( P<0.05).(3) Prognosis: the median follow-up time was 10 months (range: 0-28 months). The progression-free survival rate of TCGA molecular types were 100% (POLE ultra-mutated), 100% (MSI-H), 98% (CN-L), and 80% (CN-H) respectively and had significant differences ( P=0.034). The overall survival were 100% (POLE ultra-mutated), 100% (MSI-H), 98% (CN-L), and 90% (CN-H) respectively, but there were not statistically significant difference ( P=0.361). POLE ultra-mutated and MSI-H subgroups had the best survival, while CN-H had the worst. Conclusion:TCGA molecular classification has feasibility and clinical value in clinical application of EC, which is helpful to identify the prognosis of patients.