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.

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.

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.

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.

Benchmark Dose Assessment for Coke Oven Emissions-Induced Mitochondrial DNA Copy Number Damage Effects / 生物医学与环境科学（英文）

OBJECTIVE@#The study aimed to estimate the benchmark dose (BMD) of coke oven emissions (COEs) exposure based on mitochondrial damage with the mitochondrial DNA copy number (mtDNAcn) as a biomarker.@*METHODS@#A total of 782 subjects were recruited, including 238 controls and 544 exposed workers. The mtDNAcn of peripheral leukocytes was detected through the real-time fluorescence-based quantitative polymerase chain reaction. Three BMD approaches were used to calculate the BMD of COEs exposure based on the mitochondrial damage and its 95% confidence lower limit (BMDL).@*RESULTS@#The mtDNAcn of the exposure group was lower than that of the control group (0.60 ± 0.29 vs. 1.03 ± 0.31; P < 0.001). A dose-response relationship was shown between the mtDNAcn damage and COEs. Using the Benchmark Dose Software, the occupational exposure limits (OELs) for COEs exposure in males was 0.00190 mg/m 3. The OELs for COEs exposure using the BBMD were 0.00170 mg/m 3 for the total population, 0.00158 mg/m 3 for males, and 0.00174 mg/m 3 for females. In possible risk obtained from animal studies (PROAST), the OELs of the total population, males, and females were 0.00184, 0.00178, and 0.00192 mg/m 3, respectively.@*CONCLUSION@#Based on our conservative estimate, the BMDL of mitochondrial damage caused by COEs is 0.002 mg/m 3. This value will provide a benchmark for determining possible OELs.

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.

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.

Detection of Genetic Alterations in Oral Squamous Cell Carcinoma Using Multiplex LigationDependent Probe Amplification (MLPA)

@#Deletions and amplifications of genes often occur during multistep progression from oral precancer, seen as oral epithelial dysplasia (OED) to cancerous stage. These genetic alterations could be used as markers to aid in detection of oral squamous cell carcinomas (OSCC). This study explored the use of multiplex ligation-dependent probe amplification (MLPA) technique in detecting OSCC and OED specific genetic alterations. MLPA was used to detect gains and losses of 106 genes in DNA extracted from frozen tissue samples of 10 OSCC and 10 noncancer patients. Two biopsies of OED were analyzed to explore the alterations in oral potentially malignant disorders. There were significant differences (p<0.001) in the number of alterations in OSCC and dysplasia compared to non-cancer samples respectively. The most frequently altered genes in OSCC were PTP4A3, RECQL4, ATM, and KLK3 (60%). Five genes (MYC, SLA, TNFRSF1A, MESDC1, MIF) were altered in 50% of OSCC samples. These nine genes were specific to OSCC samples (p<0.05). Some genes, including MYB, MET, CASP2, SLA and PTEN occurred in 50% of OED samples. MLPA was able to detect genetic alterations, that are present only in the OSCC samples and showed potential to be used as an adjunctive tool in early diagnosis of OSCC.

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.

Parental origin of prenatally diagnosed pathogenic copy number variation in 56 pedigrees / 中华围产医学杂志

Objective:To investigate the prenatal management for pathogenic copy number variation (CNV) by analyzing the parental origin of CNV and pregnancy outcomes in 56 pedigrees.Methods:This study retrospectively analyzed the information of patients who received interventional prenatal diagnosis and chromosomal microarray analysis (CMA) at Guangzhou Women and Children's Medical Center from January 2015 to December 2020. The cases with pathogenic CNV indicated by CMA and receiving parental CMA for further verification were finally enrolled. Clinical data including prenatal diagnostic indications, chromosomal distribution of the pathogenic fragments and fragment sizes were collected and analyzed using t test. All cases were followed up by telephone and record review. Results:Fifty-six cases were included in this study. Pathogenic CNV in 13 (23.2%, 13/56) fetuses were inherited from one parent (eight from mothers and five from fathers), and mainly located in chromosomes 22 (3/13), 17 (3/11), 16 (2/7), 1 (2/4), and X (3/6) with fragment sizes all less than 3 Mb. The fragment size of inherited pathogenic CNV was significantly smaller than that of de novo CNV [1.69 (1.36-2.22) vs 7.54 (2.11-12.30) Mb, t=3.47, P=0.001]. Among the 43 cases with de novo pathogenic CNV, seven (16.3%) were lost to follow up and 35 (97.2%) terminated the pregnancy. The other one with a 0.58 Mb microruplication at 16p11.2 indicated at 37 gestational weeks gave birth to a baby weighting 2 900 g at 39 gestational weeks and no abnormalities were reported during an eight-month telephone follow-up. Two out of the 13 cases with inherited pathogenic CNV were lost to follow up and six pregnancies were terminated. The other five pregnancies were continued and babies were delivered with no abnormalities during a median follow-up period of 13 (4-15) months. Conclusion:Pathogenic CNV alone should not be the indication for pregnancy termination.

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.

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.

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.

Detection of copy number variation in fetuses with congenital anomalies of kidney and urinary tract / 中华围产医学杂志

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.

Parental origin verification through chromosomal microarray analysis to determine the clinical significance of copy number variations / 中华围产医学杂志

Objective:To explore the role of parental origin verification in chromosomal microarray analysis (CMA) on the determination of the clinical significance of copy number variations (CNVs).Methods:This retrospective study collected clinical information from 73 core families who underwent prenatal diagnosis at Peking University First Hospital from November 2017 to December 2019. Indications for prenatal diagnosis included ultrasound abnormality in 54 cases (including 12 with thickened nuchal translucency (≥2.5 mm), four with fetal growth restriction, seven with abnormal pregnancy history, and 31 with isolated ultrasound abnormality), NIPT indicated high-risk in four cases, advanced age in nine cases, abnormal pregnancy history alone in three cases, intrauterine death in two cases and one with maternal mental retardation. Genomic DNA of amniotic fluid sample, chorionic villi, cord blood, fetal tissues, and fetal heart blood were extracted using genomic DNA extraction kit. The CNVs of prenatal samples in 73 subjects were analyzed using array-based comparative genomic hybridization (array-CGH) analysis and single nucleotide polymorphism array (SNP-array). Peripheral blood DNA of the couples, and relevant families if necessary, were collected and analyzed in the same way. The results of parental origin detection in CMA were summarized.Results:A total of 76 CNVs were detected in these 73 samples, out of which nine were pathogenic and parental origin detection revealed that six were de novo, two were maternally, and one was paternally inherited; six CNVs were likely pathogenic, including three de novo, two maternally inherited and one paternally inherited; 20 CNVs were variants of uncertain significance, including five paternally inherited, three maternally inherited and 12 de novo; 41 CNVs were likely benign, among which 38 were inherited from parents with normal phenotype. Conclusions:Parental origin verification plays an important role in explaining the clinical significance of detected fetal CNVs and thereby can help to analyze its clinical effect and reproductive risk.

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.

Variantes en el número de copias en trastornos del neurodesarrollo, síndrome malformativo y talla baja en Perú / Copy number variation in development disorders, malformative syndrome and short stature in Peru

RESUMEN Objetivo : determinar las variantes en el número de copias y regiones de homocigosidad mediante el análisis cromosómico por micromatrices, en niños con diagnóstico de trastorno del neurodesarrollo: retraso del desarrollo psicomotor (RDPM), discapacidad intelectual (DI) y trastorno del espectro autista (TEA), así como pacientes con síndrome malformativo (SM) y talla baja idiopática (TBI). Materiales y métodos : se evaluaron a 367 niños peruanos diagnosticados clínicamente con DI, RDPM, TEA, TBI y SM a quienes se les realizó el análisis cromosómico por micromatrices (CMA 750K CGH+SNP) en sangre periférica, entre los años 2016-2018. Resultados : las edades fluctuaron entre los 4,8 meses y los 18 años, con una media de 5,6 años. Los diagnósticos más frecuentes fueron RDPM (48%) y DI (30%). Se reportaron resultados anormales (variantes patogénicas, probablemente patogénicas, disomías uniparentales y regiones de homocigosidad superiores a 2,56%) en el 50,3% de los pacientes. Los resultados anormales se observaron en el 53,3% de los casos con diagnóstico de DI y el 47,9% de RDPM; mientras que en el resto de los casos con TBI sindrómica, SM y TEA tuvieron resultados anormales en el 52,4%, 52% y 20% respectivamente. Por otro lado, encontramos hasta un 6,2% de los padres eran consanguíneos no declarados. Conclusiones : la tasa de detección de las variantes en el número de copias (CNVs) encontrada en nuestro estudio fue superior a la reportada en estudios internacionales independientemente del diagnóstico clínico. Además, se pudo encontrar una mayor frecuencia de consanguinidad no declarada con relación a estudios anteriores.

ABSTRACT Objective: To establish the ratios of the copy number variations and regions of homozygosity through chromosomal microarray analysis (CMA) in children with neurodevelopmental disorders: development delay (DD), intellectual disability (ID), and/or autistic spectrum disorder (ASD), malformative syndrome (MS) and idiopathic short stature (ISS). Materials and Methods: We evaluated 367 Peruvian children diagnosed clinically with ID, DD, ASD, ISS and MS to whom performed chromosomal microarray analysis in peripheral blood (750K CGH + SNP), between the years 2016-2018. Results: Patients' age fluctuated between 4.8 months and 18 years old, with an average of 5.6 years old. The most frequent diagnoses were development delay (48%) and intellectual disability (30%). Abnormal results (pathogenic variants, likely pathogenic variants, uniparental disomies and loss of heterozygosity> 2.5%) were reported in 50.3%. The 53.28% of the cases with a diagnosis of intellectual disability and 47.92% of development delay showed abnormal results; while the children with short stature syndromic, malformative syndrome, and autistic disorders spectrum disorders showed abnormal results in 52.38%, 52% and 20% respectively. Additionally, we found that 6.25% of parents were non-declared consanguinity. Conclusions: Abnormal results found in our study was a higher ratio than other international reports regardless of the clinical diagnosis. Furthermore, we show a most rate of non-declared consanguinity in relation with previous reports.

Relationships between blood leukocyte mitochondrial DNA copy number and inflammatory cytokines in knee osteoarthritis / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Osteoarthritis (OA) is a degenerative articular disorder manifested by cartilage destruction, subchondral sclerosis, osteophytes, and synovitis, resulting in chronic joint pain and physical disability in the elderly. The purpose of this study was to investigate mitochondrial DNA copy number (mtDNACN) and inflammatory cytokines in primary knee OA patients and healthy volunteers. A total of 204 knee OA patients and 169 age-matched healthy volunteers were recruited. Their relative blood leukocyte mtDNACN was assessed by quantitative real-time polymerase chain reaction (qRT-PCR), and ten inflammatory cytokines in their plasma were detected by multiplex immunoassay. Blood leukocyte mtDNACN in the OA group was significantly lower than that in the control group. Leukocyte mtDNACN in the control group was negatively correlated with their age (r=−0.380, P<0.0001), whereas mtDNACN in the OA group was positively correlated with their age (r=0.198, P<0.001). Plasma interleukin-4 (IL-4) and IL-6 were significantly higher in the knee OA group than in the control group. The plasma IL-6 level was positively correlated with blood leukocyte mtDNACN in the OA group (r=0.547, P=0.0014). IL-5 showed as a major factor (coefficient 0.69) in the second dimension of principle components analysis (PCA)-transformed data and was significantly higher in the OA group (P<0.001) as well as negatively correlated with mtDNACN (r=−0.577, P<0.001). These findings suggest that elevation of plasma IL-4 and IL-6 and a relative reduction in mtDNACN might be effective biomarkers for knee OA. IL-5 is a plausible factor responsible for decreasing blood leukocyte mtDNACN in knee OA patients.