研究报告

基于散发耳聋核心家系的基因新发突变(DNM)特征分析及遗传咨询策略

展开
  • 1.中国人民解放军总医院第六医学中心耳鼻咽喉头颈外科医学部,北京 100048
    2.国家耳鼻咽喉疾病临床医学研究中心,北京 100048
关静,博士,主任医师、副教授,研究方向:聋病遗传学诊断与遗传咨询。E-mail: ggy3u@126.com;
王秋菊,博士,主任医师、教授,研究方向:耳内科学及遗传性耳聋诊断与咨询。E-mail: wqcr301@vip.sina.com

收稿日期: 2024-09-14

  修回日期: 2024-12-23

  网络出版日期: 2025-01-06

基金资助

国家自然科学基金项目(82271171);国家自然科学基金项目(82271189);国家自然科学基金项目(82222016)

Interpretation of de novo mutations (DNM) and genetic counseling for sporadic hearing loss based on family trio-based sequencing

Expand
  • 1. Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing 100048,China
    2. National Clinical Research Center for Otolaryngologic Diseases, Beijing 100048, China

Received date: 2024-09-14

  Revised date: 2024-12-23

  Online published: 2025-01-06

Supported by

National Natural Science Foundation of China(82271171);National Natural Science Foundation of China(82271189);National Natural Science Foundation of China(82222016)

摘要

新发突变(de novo mutation, DNM)是导致散发耳聋的重要遗传因素,也是复杂耳聋综合征发病的重要致病原因。为了分析散发耳聋DNM遗传学特征及其致病因素,本文以2015年10月~2023年10月纳入“中国聋病基因组计划”的410个散发耳聋核心家系为对象,对收集到的先证者及其父母的临床信息进行了回顾性分析,同时通过靶向捕获高通量测序、线粒体基因组及全基因组拷贝数变异检测,进行了“父+母+先证者”核心家系遗传学比对分析,应用同源等位基因检测方法来计算DNM先证者核心家系成员之间关系系数。结果发现,这些散发耳聋核心家系中有7.3%(30例)先证者携带17种常染色体显性基因新发SNV、Indel和1种新发拷贝数变异,涵盖所有DNM类型,其中WFS1c.2051C>T、ATP1A3 c.2452G>A、ACTG1 c.94C>T是散发耳聋中常见DNM,基因型C>T变异占比最高(34.6%);临床特征分析也显示有56.7%(17/30)先证者为非综合征性耳聋,但其中有半数以上(52.9%,9/17)携带明确与“综合征性耳聋”相关的致病基因型,可能存在暂时性“拟”非综合征性耳聋表型特征。本组30例先证者父母的平均生育年龄分别为29.4岁和28.3岁,其中父亲或母亲生育年龄≥35岁的各占13.3%;同时在遗传咨询的先证者家庭结构中,63.3%为独生子女家庭且有明确再生育意愿,16.7%先证者父母为孕育“二孩”产前遗传咨询。遗传咨询时,需要以“父+母+先证者”核心家系为单位进行检测,以便分析DNM在聋病发生中的遗传贡献度;由于DNM发生与父母生育年龄的增加存在一定相关性,因此对于已生育DNM散发耳聋患者家庭,还需要采集听力健康父母的生育年龄及孕产史等临床信息,当这些家庭再生育时建议受孕后进行已明确DNM致病变异的产前诊断并重视妊娠结局。

本文引用格式

关静, 吴萧男, 李进, 谌国会, 王洪阳, 王秋菊 . 基于散发耳聋核心家系的基因新发突变(DNM)特征分析及遗传咨询策略[J]. 遗传, 2025 , 47(3) : 329 -341 . DOI: 10.16288/j.yczz.24-228

Abstract

De novo mutations (DNMs) are significant genetic factors contributing to sporadic hearing loss (HL) and complex HL syndromes. To analyze the genetic counseling characteristics and interpretation of pathogenic DNMs for sporadic HL, we retrospectively analyze the clinical information of probands and their parents from 410 sporadic HL core pedigrees enrolled in the “Chinese Deafness Genome Project (CDGP)” between October 2015 and October 2023. We apply family trio-based genome sequencing (targeted gene capture and high throughput sequencing, mitochondrial genome sequencing, and copy number variants analysis) and validate the samples of their unaffected-parents. Homologous allele sequencing is used to identity by descent (IBD) in the DNM family trios. The results reveal that 7.3% (30 cases) of the probands in these sporadic hearing loss core pedigrees carry 17 types of autosomal dominant gene de novo single nucleotide variants (SNVs), insertions/deletions (Indels), and one type of de novo copy number variation, encompassing all types of DNM. Among them, WFS1 c.2051C>T, ATP1A3 c.2452G>A, and ACTG1 c.94C>T are common DNM in sporadic HL. The genotype C>T transversion exhibit a high number (34.6%). Clinical feature analyses also show that 56.7% (17/30) of the probands have non-syndromic HL, but more than half of them (52.9%, 9/17) carry pathogenic genotypes clearly associated with “syndromic HL”, possibly exhibiting temporary "mimic" non-syndromic HL phenotypic characteristics. The average parental ages at childbirth for the 30 probands are 29.4 years for fathers and 28.3 years for mothers, with 13.3% of fathers or mothers aged ≥35 years. Additionally, among the family structure of the proband of genetic counseling, 63.3% are single-child families with a clear desire for another child, and 16.7% of the probands’ parents seek prenatal genetic counseling for conceiving a “second child”. During genetic counseling, it is essential to test the “family proband-parents’ trios” core pedigree as a unit to analyze the genetic contribution of DNMs to HL. Furthermore, there is a certain correlation between the occurrence of DNMs and increasing parental age at childbirth. Therefore, for families with a history of DNM-associated sporadic HL, it is necessary to collect clinical information such as the parental age at childbirth and obstetric history of hearing-healthy parents. For these families planning another child, it is recommended to undergo prenatal diagnosis for the identified DNM pathogenic variations after conception and pay attention to the pregnancy outcome.

参考文献

[1] Rahbari R, Wuster A, Lindsay SJ, Hardwick RJ, Alexandrov LB, Turki SA, Dominiczak A, Morris A, Porteous D, Smith B, Stratton MR, UK10K Consortium, Hurles ME. Timing, rates and spectra of human germline mutation. Nat Genet, 2016, 48(2): 126-133.
[2] Acuna-Hidalgo R, Veltman JA, Hoischen A. New insights into the generation and role of de novo mutations in health and disease. Genome Biol, 2016, 17(1): 241.
[3] Ambalavanan A, Girard SL, Ahn K, Zhou SR, Dionne- Laporte A, Spiegelman D, Bourassa CV, Gauthier J, Hamdan FF, Xiong L, Dion PA, Joober R, Rapoport J, Rouleau GA. De novo variants in sporadic cases of childhood onset schizophrenia. Eur J Hum Genet, 2016, 24(6): 944-948.
[4] Guan J, Li J, Chen GH, Shi T, Lan L, Wu XN, Zhao C, Wang DY, Wang HY, Wang QJ. Family trio-based sequencing in 404 sporadic bilateral hearing loss patients discovers recessive and De novo genetic variants in multiple ways. Eur J Med Genet, 2021, 64(10): 104311.
[5] Baux D, Vaché C, Blanchet C, Willems M, Baudoin C, Moclyn M, Faugère V, Touraine R, Isidor B, Dupin- Deguine D, Nizon M, Vincent M, Mercier S, Calais C, García-García G, Azher Z, Lambert L, Perdomo-Trujillo Y, Giuliano F, Claustres M, Koenig M, Mondain M, Roux AF. Combined genetic approaches yield a 48% diagnostic rate in a large cohort of French hearing-impaired patients. Sci Rep, 2017, 7(1): 16783.
[6] Cabanillas R, Di?eiro M, Cifuentes GA, Castillo D, Pruneda PC, álvarez R, Sánchez-Durán N, Capín R, Plasencia A, Viejo-Díaz M, García-González N, Hernando I, Llorente JL, Repáraz-Andrade A, Torreira-Banzas C, Rosell J, Govea N, Gómez-Martínez JR, Nú?ez-Batalla F, Garrote JA, Mazón-Gutiérrez á, Costales M, Isidoro- García M, García-Berrocal B, Ordó?ez GR, Cadi?anos J. Comprehensive genomic diagnosis of non-syndromic and syndromic hereditary hearing loss in Spanish patients. BMC Med Genomics, 2018, 11(1): 58.
[7] Klimara MJ, Nishimura C, Wang DH, Kolbe DL, Schaefer AM, Walls WD, Frees KL, Smith RJH, Azaiez H. De novo variants are a common cause of genetic hearing loss. Genet Med, 2022, 24(12): 2555-2567.
[8] Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, Sigurdsson A, Jonasdottir A, Jonasdottir A, Wong WSW, Sigurdsson G, Walters GB, Steinberg S, Helgason H, Thorleifsson G, Gudbjartsson DF, Helgason A, Magnusson OT, Thorsteinsdottir U, Stefansson K. Rate of de novo mutations and the importance of father's age to disease risk. Nature, 2012, 488(7412): 471-475.
[9] Guan J, He L, Yang SM, Wang QJ. Expert consensus on genetic counseling for hearing loss. Chin J Otol, 2022, 20(2): 222-226.
  关静, 贺林, 杨仕明, 王秋菊. 聋病遗传咨询专家共识. 中华耳科学杂志, 2022, 20(2): 222-226.
[10] Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL, ACMG Laboratory Quality Assurance Committee. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med, 2015, 17(5): 405-424.
[11] Oza AM, DiStefano MT, Hemphill SE, Cushman BJ, Grant AR, Siegert RK, Shen J, Chapin A, Boczek NJ, Schimmenti LA, Murry JB, Hasadsri L, Nara K, Kenna M, Booth KT, Azaiez H, Griffith A, Avraham KB, Kremer H, Rehm HL, Amr SS, Abou Tayoun AN, ClinGen Hearing Loss Clinical Domain Working Group. Expert specification of the ACMG/AMP variant interpretation guidelines for genetic hearing loss. Hum Mutat, 2018, 39(11): 1593-1613.
[12] Patel MJ, DiStefano MT, Oza AM, Hughes MY, Wilcox EH, Hemphill SE, Cushman BJ, Grant AR, Siegert RK, Shen J, Chapin A, Boczek NJ, Schimmenti LA, Nara K, Kenna M, Azaiez H, Booth KT, Avraham KB, Kremer H, Griffith AJ, Rehm HL, Amr SS, Tayoun ANA, ClinGen Hearing Loss Clinical Domain Working Group. Disease- specific ACMG/AMP guidelines improve sequence variant interpretation for hearing loss. Genet Med, 2021, 23(11): 2208-2212.
[13] Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL. Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genet Med, 2020, 22(2): 245-257.
[14] Wang WJ, Li J, Lan L, Xie LY, Xiong F, Guan J, Wang HY, Wang QJ. Auditory neuropathy as the initial phenotype for patients with ATP1A3 c.2452 G>A: Genotype-phenotype study and CI management. Front Cell Dev Biol, 2021, 9: 749484.
[15] Zhang QJ, Lan L, Xie LY, Zhao C, Guan J, Wang QJ. Identification of a novel mutation of SOX10 gene and analysis of the phenotype. Chin J Otorhinolaryngol Head Neck Surg, 2020, 55(11): 1050-1056.
  张秋静, 兰兰, 谢林怡, 赵翠, 关静, 王秋菊. SOX10基因新突变的鉴定及其临床表型特征分析. 中华耳鼻咽喉头颈外科杂志, 2020, 55(11): 1050-1056.
[16] Hodgkinson A, Eyre-Walker A. Variation in the mutation rate across mammalian genomes. Nat Rev Genet, 2011, 12(11): 756-766.
[17] Campbell CD, Eichler EE. Properties and rates of germline mutations in humans. Trends Genet, 2013, 29(10): 575-584.
[18] Guan J, Wu XN, Zhang J, Li J, Wang HY, Wang QJ. Global research landscape on the contribution of de novo mutations to human genetic diseases over the past 20 years: bibliometric analysis. J Neurogenet, 2024, 38(1): 9-18.
[19] Li C, Chen RY, Fan X, Luo JS, Qian JL, Wang J, Xie BB, Shen YP, Chen SK. EPHA4 haploinsufficiency is responsible for the short stature of a patient with 2q35-q36.2 deletion and Waardenburg syndrome. BMC Med Genet, 2015, 16: 23.
[20] Song J, Feng Y, Acke FR, Coucke P, Vleminckx K, Dhooge IJ. Hearing loss in Waardenburg syndrome: a systematic review. Clin Genet, 2016, 89(4): 416-425.
[21] Jónsson H, Sulem P, Kehr B, Kristmundsdottir S, Zink F, Hjartarson E, Hardarson MT, Hjorleifsson KE, Eggertsson HP, Gudjonsson SA, Ward LD, Arnadottir GA, Helgason EA, Helgason H, Gylfason A, Jonasdottir A, Jonasdottir A, Rafnar T, Frigge M, Stacey SN, Th Magnusson O, Thorsteinsdottir U, Masson G, Kong A, Halldorsson BV, Helgason A, Gudbjartsson DF, Stefansson K. Parental influence on human germline de novo mutations in 1,548 trios from Iceland. Nature, 2017, 549(7673): 519-522.
[22] Ma KX, Zhang WY, Wang X. Influence of paternal age on progeny prognosis. Chin J Obstet Gynecol, 2021, 56(3): 222-225.
  马可心, 张为远, 王欣. 父亲生育年龄对子代预后的影响. 中华妇产科杂志, 2021, 56(3): 222-225.
[23] Zhu WJ. Opportunities and challenges on fertility for aging men. Chin J Reprod Contracep, 2019, 39(6): 433-435.
  朱伟杰. 高龄男性生育研究的机遇与挑战. 中华生殖与避孕杂志, 2019, 39(6): 433-435.
[24] Lu BY, Han B, Hu HW, Long W, Wang L, Cai ZM, Wang HY, Yu B. Changes in maternal age and its influences on maternal and neonatal complications under the two-child policy. Chin J Perinat Med, 2019, 22(3): 157-163.
  陆蓓亦, 韩波, 胡慧文, 龙伟, 王丽, 蔡正茂, 王慧艳, 虞斌. 新生育政策下孕妇年龄的变化及对母婴并发症的影响. 中华围产医学杂志, 2019, 22(3):157-163.
[25] Mao YY, Hu H, Chen DY, Du YS, Fang YH, Wang SM, Li M, Zhou WJ. Association between parental characteristics during peri-conceptional period and risk of autism spectrum disorders in children. Chin J Reprod Contracep, 2022, 42(4): 372-378.
  毛燕燕, 胡宏, 陈东燕, 杜亚松, 房宇航, 王尚明, 李敏, 周维谨. 父母亲生育年龄等围孕期因素与儿童孤独症谱系障碍的关联性. 中华生殖与避孕杂志, 2022, 42(4): 372-378.
[26] Acuna-Hidalgo R, Bo T, Kwint MP, van de Vorst M, Pinelli M, Veltman JA, Hoischen A, Vissers LELM, Gilissen C. Post-zygotic point mutations are an underrecognized source of de novo genomic variation. Am J Hum Genet, 2015, 97(1): 67-74.
[27] Qin L, Wang J, Tian X, Yu H, Truong C, Mitchell JJ, Wierenga KJ, Craigen WJ, Zhang VW, Wong LJC. Detection and quantification of mosaic mutations in disease genes by next-generation sequencing. J Mol Diagn, 2016, 18(3): 446-453.
[28] Gambin T, Liu Q, Karolak JA, Grochowski CM, Xie NG, Wu LR, Yan YH, Cao Y, Coban Akdemir ZH, Wilson TA, Jhangiani SN, Chen E, Eng CM, Muzny D, Posey JE, Yang YP, Zhang DY, Shaw C, Liu PF, Lupski JR, Stankiewicz P. Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. Genet Med, 2020, 22(11): 1768-1776.
[29] Sim JCH, White SM, Lockhart PJ. ARID1B-mediated disorders: Mutations and possible mechanisms. Intractable Rare Dis Res, 2015, 4(1): 17-23.
[30] van Ravenswaaij-Arts C, Martin DM. New insights and advances in CHARGE syndrome: Diagnosis, etiologies, treatments, and research discoveries. Am J Med Genet C Semin Med Genet, 2017, 175(4): 397-406.
[31] Boothe M, Morris R, Robin N. Stickler syndrome: a review of clinical manifestations and the genetics evaluation. J Pers Med, 2020, 10(3): 105.
[32] Aldè M, Cantarella G, Zanetti D, Pignataro L, La Mantia I, Maiolino L, Ferlito S, Di Mauro P, Cocuzza S, Lechien JR, Iannella G, Simon F, Maniaci A. Autosomal dominant non-syndromic hearing loss (DFNA): a comprehensive narrative review. Biomedicines, 2023, 11(6): 1616.
[33] Pauli RM. Achondroplasia: a comprehensive clinical review. Orphanet J Rare Dis, 2019, 14(1): 1.
[34] Wang L, Lin QF, Wang HY, Guan J, Lan L, Xie LY, Yu L, Yang J, Zhao C, Liang JL, Zhou HL, Yang HM, Xiong WP, Zhang QJ, Wang DY, Wang QJ. Clinical auditory phenotypes associated with GATA3 gene mutations in familial hypoparathyroidism-deafness-renal dysplasia syndrome. Chin Med J (Engl), 2017, 130(6): 703-709.
[35] Li XH, Huang SS, Wang GJ, Kang DY, Han MY, Wu XD, Yang JY, Zheng QC, Zhao CY, Yuan YY, Dai P. Quantitative assessment of low-level parental mosaicism of SNVs and CNVs in Waardenburg syndrome. Hum Genet, 2023, 142(3): 419-430.
[36] Ruiz-Pérez MV, Henley AB, Arsenian-Henriksson M. The MYCN Protein in health and disease. Genes (Basel), 2017, 8(4): 113.
[37] Gregory GE, Munro KJ, Couper KN, Pathmanaban ON, Brough D. The NLRP3 inflammasome as a target for sensorineural hearing loss. Clin Immunol, 2023, 249: 109287.
[38] Wang HY, Guan LP, Wu XN, Guan J, Li J, Li N, Wu KL, Gao Y, Bing D, Zhang JG, Lan L, Shi T, Li DY, Wang WJ, Xie LY, Xiong F, Shi W, Zhao LJ, Wang DY, Yin Y, Wang QJ. Clinical and genetic architecture of a large cohort with auditory neuropathy. Hum Genet, 2024, 143(3): 293-309.
[39] Gao X, Huang SS, Qiu SW, Su Y, Wang WQ, Xu HY, Xu JC, Kang DY, Dai P, Yuan YY. Congenital sensorineural hearing loss as the initial presentation of PTPN11- associated Noonan syndrome with multiple lentigines or Noonan syndrome: clinical features and underlying mechanisms. J Med Genet, 2021, 58(7): 465-474.
[40] Wang SQ, Chen Y, Luo KH, Shi NJ, Xiao KL, Cui ZH, Zeng TS, Li HQ. Diagnosis and genetic analysis of a case of Waardenburg syndrome type 2 with hypogonadotropic hypogonadism caused by SOX10 gene deletion. Hereditas(Beijing), 2022, 44(12): 1158-1166.
  王思琪, 陈阳, 罗宽宏, 史宁杰, 肖康丽, 崔振海, 曾天舒, 黎慧清. 一例SOX10基因缺失所致的Waardenburg综合征2型合并低促性腺激素性性腺功能减退症的诊断和基因检测分析. 遗传, 2022, 44(12): 1158-1166.
文章导航

/