A proteomic approach to investigate the qualitative and quantitative polymorphism of <i>β</i>-lactoglobulin in ovine milk: Inference on gene copy-number variations

The rationale of this work is based on recent evidences suggesting that: 1) both qualitative and quantitative β-lactoglobulin (β-LG) polymorphism may be found in bovine milk;2) quantitative polymorphisms are often the result of expression gradients in multiple copies of a gene;3) the β-LG gene is duplicated in the dog and bovine genome;4) mammary genes are highly conserved across Mammalia. Thus, an investigation was conducted on ovine β-LG polymorphism checking phenotypic evidence for copy-number variants of β-LG in sheep. To the purpose, 206 milk samples were collected, during a small-scale survey within sheep farms breeding Southern Italian breeds. PAGIF screening of the samples revealed that approximately 50% individuals exhibited β-LG polymorphism and 4 different quantitative patterns, which were characterized in detail by a proteomic approach relying on combined chromatographic and mass spectrometric techniques. The expected figures based on the expression gradient models were compared with well-established α-globin gene arrangements in sheep. The different phenotypes suggest the presence of both duplicate and triplicate BLG haplotypes. The occurrence of a triplicate haplotype was supported by population data. The current study supports the helpfulness of up-to-date proteomics for inferring copy number polymorphisms through the characterization of the phenotypic expression.

Low-depth whole genome sequencing reveals copy number variations associated with higher pathologic grading and more aggressive subtypes of lung non-mucinous adenocarcinoma

Objective:Histology grade,subtypes and TNM stage of lung adenocarcinomas are useful predictors of prognosis and survival.The aim of the study was to investigate the relationship between chromosomal instability,morphological subtypes and the grading system used in lung non-mucinous adenocarcinoma(LNMA).Methods:We developed a whole genome copy number variation(WGCNV)scoring system and applied next generation sequencing to evaluate CNVs present in 91 LNMA tumor samples.Results:Higher histological grades,aggressive subtypes and more advanced TNM staging were associated with an increased WGCNV score,particularly in CNV regions enriched for tumor suppressor genes and oncogenes.In addition,we demonstrate that 24-chromosome CNV profiling can be performed reliably from specific cell types(<100 cells)isolated by sample laser capture microdissection.Conclusions:Our findings suggest that the WGCNV scoring system we developed may have potential value as an adjunct test for predicting the prognosis of patients diagnosed with LNMA.

AB015.The relationship between copy number variations and high myopia in Chinese:a case-control study

As a complex disease,myopia is the most common eye disease worldwide.Many myopia susceptibility genes or variants have been successfully identified in the past years by genome-wide genetic association studies(GWAS),which focus mainly on the single-nucleotide polymorphisms.Little attention has been paid to examine the role of copy number variations(CNVs)in refractive error and myopia.This study adopted a systematic strategy to investigate the role of CNVs in high myopia.In the discovery phase,a pilot GWAS suggests putative CNVs for follow-up.Multiplex ligation-dependent probe amplification was then used to quantify the copy number of 89 CNV segments in 737 case-control samples in the second phase and then 24 top-ranking CNVs in a second group of 1,029 case-control samples in the final validation phase.This validation phase identified 22 significant CNVs.Further work is needed to examine the role of these few CNVs in myopia development.

CNV-seq技术在自然流产遗传学检测中的应用

目的:探讨低深度全基因组测序技术(copy number variation sequencing,CNV-seq)对于检测自然流产物中的染色体异常和拷贝数变异(copy number variations,CNVs)的应用价值。方法:对67例流产物进行CNV-seq检测,分析流产的遗传学因素。结果:本研究共检测67例流产组织,成功检测67例,成功率为100.00%,染色体结果异常共49例,异常检出率为73.13%,其中染色体数目异常28例、嵌合体8例、CNVs 13例,其中发生频率最高的四种异常依次是:45,X综合征、16-三体、21-三体和22-三体。结论:染色体异常是胚胎停育的最重要原因,CNV-seq可以检测出常规染色体异常和染色体核型分析无法发现的CNVs,推荐临床上使用对流产物进行CNV-seq检测,可以为患者提供更全面的遗传咨询。

101例胎儿性染色体非整倍体异常核型分布特征及妊娠结局分析

目的分析101例胎儿性染色体非整倍体(sex chromosome aneuploidy,SCA)异常核型分布特征及妊娠结局。方法回顾性收集2016年1月~2021年12月7821例于广西壮族自治区人民医院成功进行产前核型诊断孕妇的临床资料,均行细胞培养染色体核型分析与拷贝数变异测序(copy number variation sequencing,CNV-seq)检测,对检出的101例SCA异常胎儿病历进行分析。结果SCA共检出101例,检出率为1.29%。其中克氏综合征占比33.66%,超雌综合征占比17.82%,超雄综合征占比12.87%,特纳综合征占比10.89%,其他非整倍体异常(包括:48,XXXY 1例,69,XXY[80%]/68,XXY,-22[20%]1例)占比1.98%,嵌合体占比22.77%。101例SCA产前指征结果为:年龄≥35周岁占比53.47%(54/101),血清生化指标筛查高/临界风险占比4.95%(5/101),胎儿超声检测异常占比17.82%(18/101),无创产前基因检测(non-invasive prenatal testing,NIPT)异常占比51.49%(52/101),不良孕产史占比12.87%(13/101),其他原因(孕妇脑瘫1例、双方珠蛋白生成障碍性贫血4例)5例行产前诊断,占比4.95%(5/101),部分病例并发多项产前诊断指征。23例诊断为性染色体嵌合体的胎儿,其中有22例通过核型与CNV-seq双向验证,11例孕妇选择终止妊娠,其余选择继续妊娠。结论产前核型诊断联合血清学检测、孕期超声等不同产前筛查手段,有利于提高SCA检出率。而CNV-seq可对性染色体嵌合体孕妇的遗传咨询提供更多临床依据。

牦牛基因组拷贝数变异研究进展

拷贝数变异(copy number variation, CNV)是基因组结构变异(structural variation, SV)的重要组成部分。与SNP(single nucleotide polymorphism)相比,CNV显示出更丰富的复杂遗传变异,在家畜重要经济性状遗传机理、疾病诱因和物种进化等研究方面具有重要意义。牦牛作为青藏高原的重要牛种,近年来随着高通量测序技术的快速发展和参考基因组的不断升级,其全基因组水平上CNV的研究获得重要进展。本文在阐述基因组CNV的形成原理、作用机制和检测方法基础上,综述了近10年来牦牛基因组CNV的研究现状,分析探究了存在的一些问题与不足,并对其未来的发展和应用趋势进行了展望,以期为深入开展牦牛基因组研究和加速牦牛遗传资源的分子育种进程提供参考。

LMNB1相关常染色体显性遗传成人型脑白质营养不良家系分析

目的总结一个LMNB1相关常染色体显性遗传成人型脑白质营养不良(adult-onset autosomal dominant leukodystrophy,ADLD)家系的临床、影像学特点,并进行致病性变异分析。方法选取2023年11月首都医科大学宣武医院确诊为ADLD患者1例,收集先证者及家系其他患者的临床和影像学资料,对先证者进行全外显子组测序分析及LMNB1基因的多重连接探针扩增(multiplex ligation-dependent probe amplification,MLPA)检测,并进行致病性分析和表型匹配分析。结果本例患者(先证者)男,44岁,因“大小便障碍3年,双下肢乏力2年余”就诊,基因检测示LMNB1基因1-11号外显子重复变异,评定为致病性变异,表型与ADLD匹配,先证者(Ⅲ:9)和Ⅲ:6以自主神经功能障碍起病,系ADLD典型表现,Ⅱ:11首发症状为头部震颤,与其他患者不同。结论ADLD患者的LMNB1基因1-11号外显子重复变异,符合常染色体显性遗传方式。成年患者以自主神经功能障碍起病,随后累及小脑、锥体束,MRI示广泛对称的脑白质病变、脊髓萎缩时应考虑ADLD,建议行LMNB1基因检测。

KIT杂合大片段缺失导致斑驳病一家系的临床表型

目的鉴定一个斑驳病家系的致病基因突变。方法收集斑驳病患者及其家系成员的临床资料,采集外周血,进行全外显子组测序。通过qPCR验证目的基因的缺失;采用gap-PCR结合Sanger测序法确定具体缺失的大小以及位点。结果在先证者4号染色体上存在约1.74 Mb的杂合大片段缺失突变,其中包括了全部KIT(斑驳病的致病基因)。该缺失在家系中呈基因型-表型共分离,在dbSNV数据库中未见该区域的缺失报道。该缺失是目前报道的最小的因KIT全长缺失而导致斑驳病表型的片段缺失。结论KIT缺失是导致该家系斑驳病表型的原因。

两株黑曲霉全基因组重测序分析

为探究导致不同黑曲霉中赭曲霉毒素A(ochratoxin A,OTA)生物合成差异的原因并对毒素进行去除及防控,该研究选用黑曲霉CICC 41702与黑曲霉3.316为试验材料,利用全基因组重测序分析两株黑曲霉菌株基因组水平的差异及OTA生物合成的机制。利用Illumina技术对产和不产OTA的两株黑曲霉菌株进行全基因组重测序,并以黑曲霉CBS 513.88的基因组序列为参考,深度挖掘单核苷酸多态性(single nucleotide polymorphism,SNP)、插入或删除(insertions or deletions,InDel)、结构性变异(structural variants,SV)、拷贝数变异(copy number variation,CNV)等信息,并对参与OTA生物合成的基因进行特异性生物信息学分析。结果表明,黑曲霉3.316比黑曲霉CICC 41702显示出更高的变异,且An15g07920基因在黑曲霉3.316中存在大量的非同义突变并显示缺失了23600 bp,推测这可能是导致两株黑曲霉的OTA生物合成差异的原因。

基于低深度全基因拷贝数变异测序(CNV-Seq)的稽留流产发生次数及年龄分析

目的应用低深度全基因组拷贝数变异测序(copy number variation sequencing,CNV-Seq)检测稽留流产物(绒毛/胎儿组织)染色体,探讨胎儿绒毛/组织染色体异常与稽留流产发生次数及年龄的关系。方法应用CNV-Seq技术,对2019年2月至2021年2月在粤北人民医院妇产科就诊的208例稽留流产物(绒毛/胎儿组织)进行染色体检查。按流产次数、流产发生年龄进行分组:其中初次稽留流产76例,≥2次稽留流产127例;发生流产年龄<35岁151例,≥35岁52例。分析不同流产次数的染色体异常情况、不同年龄段染色体异常情况。结果在208例稽留流产标本中成功检测203例,检测成功率为97.60%。检出染色体异常107例,异常率为52.71%;其中初次稽留流产的染色体异常40例,异常率为52.63%,≥2次稽留流产的染色体异常67例,异常率为52.75%,<35岁的染色体异常70例,异常率为46.36%,≥35岁的染色体异常37例,异常率71.15%。初次稽留流产与≥2次稽留流产的染色体异常率比较差异无统计学意义(χ^(2)=0.00,P=1.00),<35岁与≥35岁稽留流产的染色体异常率比较差异有统计学意义(χ^(2)=9.54,P=0.01)。结论CNV-Seq技术有助于查找稽留流产的遗传学原因,对再生育指导有重要意义。染色体异常是稽留流产发生的主要原因,复发性流产的染色体异常发生率未见显著增加,高龄显著增加稽留流产染色体异常发生率。

miR-181家族基因SNPs及CNV在系统性红斑狼疮疾病的研究进展

微小RNA广泛参与多种疾病的发生发展,尤其是系统性红斑狼疮。微小RNA-181基因簇是目前发现较新的一个微小RNA,可通过多种机制参与系统性红斑狼疮的疾病活动和病情进展。笔者就miR-181基因簇单核苷酸多态性及拷贝数变异在系统性红斑狼疮疾病的研究进展进行综述。

焦虑性神经症患者关联性负变(CNV)实验研究

目的 探讨焦虑性神经症患者关联性负变 (CNV)的特点。方法 采用光和声成对刺激以及反应时间技术 ,对 2 4例焦虑性神经症患者和 2 2名正常成人的CNV进行对照研究。结果 焦虑性神经症组波形不规则 ,CNV -Ⅱ型 (延迟型 )尤甚。与正常对照组比较 ,焦虑性神经症患者CNV潜伏期A点延迟 (P <0 .0 5 ) ,波幅B降低 (P <0 .0 5 )。

The role of genomic structural variation in the genetic improvement of polyploid crops

Many of our major crop species are polyploids, containing more than one genome or set of chromosomes. Polyploid crops present unique challenges, including difficulties in genome assembly, in discriminating between multiple gene and sequence copies, and in genetic mapping, hindering use of genomic data for genetics and breeding. Polyploid genomes may also be more prone to containing structural variation, such as loss of gene copies or sequences(presence–absence variation) and the presence of genes or sequences in multiple copies(copynumber variation). Although the two main types of genomic structural variation commonly identified are presence–absence variation and copy-number variation, we propose that homeologous exchanges constitute a third major form of genomic structural variation in polyploids. Homeologous exchanges involve the replacement of one genomic segment by a similar copy from another genome or ancestrally duplicated region, and are known to be extremely common in polyploids. Detecting all kinds of genomic structural variation is challenging, but recent advances such as optical mapping and long-read sequencing offer potential strategies to help identify structural variants even in complex polyploid genomes. All three major types of genomic structural variation(presence–absence, copy-number, and homeologous exchange) are now known to influence phenotypes in crop plants, with examples of flowering time, frost tolerance, and adaptive and agronomic traits. In this review,we summarize the challenges of genome analysis in polyploid crops, describe the various types of genomic structural variation and the genomics technologies and data that can be used to detect them, and collate information produced to date related to the impact of genomic structural variation on crop phenotypes. We highlight the importance of genomic structural variation for the future genetic improvement of polyploid crops.

CNV-seq技术对1953例自然流产物的染色体数目和拷贝数变异分析

目的基于染色体拷贝数变异测序(copy number variation sequencing,CNV-seq)技术对1953例自然流产物进行遗传学检测,探讨流产组织染色体数目异常和拷贝数变异(copy number variation,CNV)在自然流产中的发生情况。方法回顾性统计分析2014年3月至2019年11月送检并行CNV-seq检测的1953例自然流产组织染色体变异分析结果。结果①1953例流产组织样本中,1013例存在染色体异常,异常率为51.87%,其中以染色体非整倍体最常见,共有870例,发生率为44.55%(870/1953),占异常核型的85.88%(870/1013),涉及除1号染色体外的所有染色体,以16-三体发生频率最高,其次为22-三体、X单体15-三体和21-三体。②本次研究发现孕妇年龄≥35岁组胚胎染色体异常率明显高于年龄<35岁组(56.57%vs.42.17%,P<0.05);早期自然流产(孕周<12周)的胚胎染色体异常率明显高于中晚期自然流产(58.76%vs.23.21%,P<0.01);而产妇既往流产次数与胚胎染色体的异常率无统计学意义(P>0.05)。结论胚胎染色体异常,尤其染色体非整倍体异常,是自然流产的主要原因,多发于孕早期,且随着孕妇年龄增长,胚胎染色体异常发生率显著升高。

CNV-seq技术检测90例发育迟缓患儿基因组拷贝数变异的遗传学分析

目的探讨发育障碍疾病患儿致病性拷贝数变异(CNV)的特征。方法收集2017至2019年诊断为发育迟缓、并经核型分析患儿的临床资料,采集患儿外周血进行基于高通量测序的低深度全基因组测序(CNV-seq)。利用ClinVar、DECIPHER、OMIM、DGV数据库注释CNV数据,依据ACMG评估CNV致病性,并通过PubMed数据库检索相关报道文献。结果检测90例患儿,CNV阳性18例,阳性率为20%。其中ACMG判定致病性,或有报道的致病性CNV 15例,可能致病CNV 3例;意义未明的CNV 32例。结论CNV是导致儿童发育迟缓的重要病因,>1 Mb的微缺失/重复具有更高致病性,可将CNV-seq作为产前诊断的重要手段,以有效防治发育障碍相关疾病。

A STUDY ON CNV OF PATIENTS WITH MENTAL RETARDATION

Objective: To investigate the variations of contingent negative variation (CNV) of petients with mental retardation. Methods: The CNV was recorded in 16 children with mental retardation (MR) and 14 healthly age-matched controls. And CNV retest was carried out in 11 children with MR after one yeat treatment of Piracetam. Results: Compared with the normal control, the CNV of MR group showed prolonged postimperative negative variation (PINV) duration (P＜0.01) and total A-C duration (P ＜ 0.01), decreased amplitude B (P＜0.01 ), and reduced preimperative A-S2 area (P＜0.01). A comparison of the CNV of MR group was made between before and after one year treatment of Piracetam and no significant difference was found. Conclusions:The significant CNV variations were found in children with MR and these abnormal changes presisted throughout the Piracetam treatment.

SMARCC1 copy number variation is related to metastatic colon cancer:an investigation based on TCGA data

Objective There are no well-defined genetic indicators for distant metastatic illness in patients with colon cancer(CC).The discovery of genetic changes linked to metastatic CC might aid in the development of systemic and local therapeutic approaches.Using The Cancer Genome Atlas(TCGA),we examined the relationship between copy number variation(CNV)of SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1(SMARCC1)and distant metastatic illness in patients with CC.Methods Genetic sequencing data of all relevant CC patients and clinical features were collected from TCGA using R.There were 506 CC patients with CNV and clinical outcome data.The CNV of SMARCC1 was examined for its correlation with distant metastatic disease using the TCGA CC dataset(M1 vs.M0).After adjusting for age,sex,T stage,N stage,adjuvant chemotherapy,microsatellite instability(MSI),and surgical margin status,univariate and multivariate logistic regression analyses were performed.Results SMARCC1 CNV was linked to distant metastatic disease(P=0.012 and 0.008 in univariate and multivariate analysis,respectively);positive lymph nodes and margin status were also associated with distal metastases(all P<0.01).MSI,T stage,N stage,adjuvant treatment,sex,race,and MSI were not associated with metastases(all P>0.05).Conclusion SMARCC1 CNV is associated with distant metastatic disease in patients with CC.In individuals with CC,such genetic profiles might be utilized therapeutically to support optimal systemic treatment options against local treatments for CC,such as radiation therapy,pending additional confirmation.

亚显微水平CNVS致病的分子机制及其检测方法与新进展

拷贝数变异(copy number variations,CNVs)是由基因组发生重排引起的,通常指长度为几千个碱基对以上的基因组片段的拷贝数增加或减少,表现为亚显微水平的缺失、重复和片段性重复等。CNVs与许多疾病相关,是导致人类出生缺陷、发育疾病和癌症等疾病的重要机制之一。深入了解基因组中的拷贝数变异对于更好地理解基因与疾病之间的关系、遗传-环境相互作用以及基因组变异与物种进化之间的关联具有重要意义。因此,与CNVs相关的疾病研究已经成为当前医学遗传学研究中的重要领域。对亚显微水平CNVs致病的分子机制、检测方法以及最新进展进行综述。

利用全基因组重测序数据检测8个鸭品种基因组拷贝数变异

旨在鉴别与鸭重要经济性状潜在相关的拷贝数变异(copy number variations,CNVs),为解析CNVs对鸭经济性状的影响提供前期研究基础。本研究利用从美国国家生物技术信息中心(National Center for Biotechnology Information,NCBI)公共数据库中下载的8个鸭品种共78个个体的全基因组重测序数据,采用CNVnator和CNVcaller软件进行全基因组CNVs检测,同时只保留两个软件检测结果中存在至少1 bp重叠的同类型CNVRs,以消除假阳性对试验结果的影响。结果显示,8个鸭品种的CNVs合并后共检测出7550个CNV regions(CNVRs),其中包括7098个duplications和452个deletions。这些CNVRs在鸭29条常染色体上呈不均匀分布,总长度为16111.2 kb,平均长度为2134 bp,约占鸭基因组的1.51%。此外,本研究在8个鸭品种共筛选到4304个潜在的品种特异性CNVRs,覆盖1230个注释基因。通过基因功能Gene Ontology(GO)富集分析,鉴别到38个可能与生长和繁殖相关的CNVRs。本研究共发现7550个CNVRs,筛选出4304个潜在的品种特异性CNVRs,并鉴别到38个与鸭生长和繁殖潜在相关的CNVRs,为深入探究CNVs对鸭重要经济性状的影响提供了必要的研究基础。

拷贝数变异测序与Q-PCR检测巨细胞病毒感染一致性的比较

目的 比较拷贝数变异测序(CNV-seq)与Q-PCR在测定先天性巨细胞病毒(cytomegalovirus, CMV)感染方面是否存在一致性。方法 选取自2020年至2022年以来在海南省海南医学院第一附属医院产前诊断中心就诊过的9位患者的羊水进行两种检测技术的对比检测,合并患者的临床资料,进行总结。结果 CNV-seq与Q-PCR均提示1例患者CMV感染阳性,且为同一例;8例检测样本CNV-seq和Q-PCR结果显示均为阴性,表明其妊娠异常可能并非感染CMV导致,且检测结果呈现阴性并不能完全排除感染CMV。结论 CNV-seq与Q-PCR在测定先天性CMV感染方面可能存在一致性。