CCMG practice guideline: laboratory guidelines for next-generation sequencing.

Abstract:

:PurposeThe purpose of this document is to provide guidance for the use of next-generation sequencing (NGS, also known as massively parallel sequencing or MPS) in Canadian clinical genetic laboratories for detection of genetic variants in genomic DNA and mitochondrial DNA for inherited disorders, as well as somatic variants in tumour DNA for acquired cancers. They are intended for Canadian clinical laboratories engaged in developing, validating and using NGS methods. METHODS OF STATEMENT DEVELOPMENT: The document was drafted by the Canadian College of Medical Geneticists (CCMG) Ad Hoc Working Group on NGS Guidelines to make recommendations relevant to NGS. The statement was circulated for comment to the CCMG Laboratory Practice and Clinical Practice committees, and to the CCMG membership. Following incorporation of feedback, the document was approved by the CCMG Board of Directors. DISCLAIMER: The CCMG is a Canadian organisation responsible for certifying medical geneticists and clinical laboratory geneticists, and for establishing professional and ethical standards for clinical genetics services in Canada. The current CCMG Practice Guidelines were developed as a resource for clinical laboratories in Canada and should not be considered to be inclusive of all information laboratories should consider in the validation and use of NGS for a clinical laboratory service.

journal_name

J Med Genet

authors

Hume S,Nelson TN,Speevak M,McCready E,Agatep R,Feilotter H,Parboosingh J,Stavropoulos DJ,Taylor S,Stockley TL,Canadian College of Medical Geneticists (CCMG).

doi

10.1136/jmedgenet-2019-106152

subject

Has Abstract

pub_date

2019-12-01 00:00:00

pages

792-800

issue

12

eissn

0022-2593

issn

1468-6244

pii

jmedgenet-2019-106152

journal_volume

56

pub_type

杂志文章
  • Disease associated balanced chromosome rearrangements: a resource for large scale genotype-phenotype delineation in man.

    abstract::Disease associated balanced chromosomal rearrangements (DBCRs), which truncate, delete, or otherwise inactivate specific genes, have been instrumental for positional cloning of many disease genes. A network of cytogenetic laboratories, Mendelian Cytogenetics Network (MCN), has been established to facilitate the identi...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.37.11.858

    authors: Bugge M,Bruun-Petersen G,Brøndum-Nielsen K,Friedrich U,Hansen J,Jensen G,Jensen PK,Kristoffersson U,Lundsteen C,Niebuhr E,Rasmussen KR,Rasmussen K,Tommerup N

    更新日期:2000-11-01 00:00:00

  • Evaluation of a counselling protocol for predictive genetic testing for hereditary non-polyposis colorectal cancer.

    abstract:OBJECTIVES:To evaluate the feasibility of a reduced counselling programme for predictive genetic testing for hereditary non-polyposis colorectal cancer (HNPCC) in terms of counsellees' opinions on the extent and significance of genetic counselling and need for psychological support at different phases of the testing pr...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.37.2.108

    authors: Aktan-Collan K,Mecklin JP,de la Chapelle A,Peltomäki P,Uutela A,Kääriäinen H

    更新日期:2000-02-01 00:00:00

  • Submicroscopic deletions at 16p13.3 in Rubinstein-Taybi syndrome: frequency and clinical manifestations in a North American population.

    abstract::Rubinstein-Taybi syndrome (RTS) is a well delineated multiple congenital anomaly syndrome characterised by mental retardation, broad thumbs and toes, short stature, and specific facial features. The recent localisation of the disorder to 16p13.3 and subsequent identification of a submicroscopic deletion of this region...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.34.3.203

    authors: Wallerstein R,Anderson CE,Hay B,Gupta P,Gibas L,Ansari K,Cowchock FS,Weinblatt V,Reid C,Levitas A,Jackson L

    更新日期:1997-03-01 00:00:00

  • First trimester fetal diagnosis of genetic disorders: clinical evaluation of 250 cases.

    abstract::Chromosome and enzyme determinations were performed in 250 pregnancies between the 7th and the 12th week of gestation. The majority of the tests were performed for risk of chromosomal abnormalities and 75% of the women were 35 years old or more. We describe a chorionic villi sampling (CVS) technique which proved to be...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.22.2.92

    authors: Brambati B,Simoni G,Danesino C,Oldrini A,Ferrazzi E,Romitti L,Terzoli G,Rossella F,Ferrari M,Fraccaro M

    更新日期:1985-04-01 00:00:00

  • Novel LMNA mutations cause an aggressive atypical neonatal progeria without progerin accumulation.

    abstract:BACKGROUND:Progeroid syndromes are genetic disorders that recapitulate some phenotypes of physiological ageing. Classical progerias, such as Hutchinson-Gilford progeria syndrome (HGPS), are generally caused by mutations in LMNA leading to accumulation of the toxic protein progerin and consequently, to nuclear envelope ...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmedgenet-2015-103695

    authors: Soria-Valles C,Carrero D,Gabau E,Velasco G,Quesada V,Bárcena C,Moens M,Fieggen K,Möhrcken S,Owens M,Puente DA,Asensio Ó,Loeys B,Pérez A,Benoit V,Wuyts W,Lévy N,Hennekam RC,De Sandre-Giovannoli A,López-Otín C

    更新日期:2016-11-01 00:00:00

  • Hunter syndrome presenting as macrocephaly and hydrocephalus.

    abstract::A 2-year-old boy with macrocephaly, communicating hydrocephalus, and mild hepatosplenomegaly was found to have mild Hunter syndrome (MPS II). Establishment of the latter diagnosis was complicated by the paucity of obvious physical findings because of the patient's young age and his ethnic origin. ...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.14.6.445

    authors: Yatziv S,Epstein CJ

    更新日期:1977-12-01 00:00:00

  • Cost effectiveness of DNA diagnosis for four monogenic diseases.

    abstract::In this paper the costs and benefits associated with DNA diagnosis of subjects who are at risk of having a child with a monogenic disease and who seek genetic counselling because of their reproductive plans are predicted under various assumptions using a mathematical model. Four monogenic diseases have been considered...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.34.9.741

    authors: van der Riet AA,van Hout BA,Rutten FF

    更新日期:1997-09-01 00:00:00

  • Phenotypic and quantitative relationship of red cell acid phosphatase with haemoglobin, haptoglobin, and G6PD phenotypes.

    abstract::The phenotypic and quantitative relationship of red cell acid phosphatase with haemoglobin, haptoglobin, and G6PD phenotypes was investigated in three populations in the Sudan and one population in Nilgiris, India. No significant consistent association of red cell acid phosphatase phenotypes was observed with these po...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.18.4.271

    authors: Saha N,Patgunarajah N

    更新日期:1981-08-01 00:00:00

  • Severe intrauterine growth retardation, blepharophimosis, and cylindrical nose with midline groove: a new syndrome?

    abstract::A malformed female infant is described. In addition to cardiac, renal, and skeletal (rib) anomalies, severe intrauterine growth retardation and distinct facial dysmorphism were present. The question is raised whether this child represents a new syndrome. ...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.30.6.525

    authors: de Die-Smulders CE,Droog RP,van Dijk M,Fryns JP

    更新日期:1993-06-01 00:00:00

  • Clinical, molecular and histopathological features of short stature syndrome with novel CUL7 mutation in Yakuts: new population isolate in Asia.

    abstract:BACKGROUND:In total, 43 patients having short stature syndrome in 37 Yakut families with autosomal recessive prenatal and postnatal nonprogressive growth failure and facial dysmorphism but with normal intelligence have been identified. METHODS:Because Yakuts are considered as a population isolate and the disease is ra...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.2007.051979

    authors: Maksimova N,Hara K,Miyashia A,Nikolaeva I,Shiga A,Nogovicina A,Sukhomyasova A,Argunov V,Shvedova A,Ikeuchi T,Nishizawa M,Kuwano R,Onodera O

    更新日期:2007-12-01 00:00:00

  • Report of a critical recombination further narrowing the TSC1 region.

    abstract::A large tuberous sclerosis multigenerational family segregating with markers on chromosome 9q from the TSC1 region was studied with a new highly polymorphic marker (designated A6) from the region. A critical affected person showed recombination with the marker, eliminating approximately 100 kilobases from the telomeri...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.33.7.559

    authors: Au KS,Murrell J,Buckler A,Blanton SH,Northrup H

    更新日期:1996-07-01 00:00:00

  • Rhabdomyosarcoma in patients with constitutional mismatch-repair-deficiency syndrome.

    abstract:BACKGROUND:Biallelic germline mutations in the mismatch repair genes MLH1, MSH2, MSH6 or PMS2 cause a recessive childhood cancer syndrome characterised by early-onset malignancies and signs reminiscent of neurofibromatosis type 1 (NF1). Alluding to the underlying genetic defect, we refer to this syndrome as constitutio...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.2008.064212

    authors: Kratz CP,Holter S,Etzler J,Lauten M,Pollett A,Niemeyer CM,Gallinger S,Wimmer K

    更新日期:2009-06-01 00:00:00

  • Genetic study of congenital heart defects in Northern Ireland (1974-1978).

    abstract::Congenital heart defects are a major congenital abnormality and are assuming increasing importance. A study was undertaken to estimate the incidence of congenital heart defects in Northern Ireland over a five year period (1974-1978), to determine the age at diagnosis and to assess the risk of recurrence in sibs. An in...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.31.11.858

    authors: Hanna EJ,Nevin NC,Nelson J

    更新日期:1994-11-01 00:00:00

  • Risk of breast cancer in male BRCA2 carriers.

    abstract::The risk of breast cancer for unaffected men who test positive for a BRCA2 mutation is based on very few retrospective studies. We have used both retrospective and prospective analysis in 321 families with pathogenic BRCA2 mutations. Three breast cancers occurred in male first-degree relatives after family ascertainme...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.2009.075176

    authors: Evans DG,Susnerwala I,Dawson J,Woodward E,Maher ER,Lalloo F

    更新日期:2010-10-01 00:00:00

  • Oculoauriculovertebral spectrum and cerebral anomalies.

    abstract::We report on three Dutch children with a clinical diagnosis of oculoauriculovertebral spectrum (OAVS) and hydrocephalus. The clinical features are compared to 15 published cases of OAVS and hydrocephalus. Several other cerebral abnormalities were present in the whole group. About half of the cases had cleft lip/palate...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章,评审

    doi:10.1136/jmg.29.5.326

    authors: Schrander-Stumpel CT,de Die-Smulders CE,Hennekam RC,Fryns JP,Bouckaert PX,Brouwer OF,da Costa JJ,Lommen EJ,Maaswinkel-Mooy PD

    更新日期:1992-05-01 00:00:00

  • Detecting low penetrance genes in cancer: the way ahead.

    abstract::The search for the genes responsible for many complex genetic diseases is well under way and has already been successful in some cases. The study of cancer as a complex genetic disease has lagged behind other conditions, largely because of particular problems that are associated with malignant disease. Cancer also, ho...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章,评审

    doi:10.1136/jmg.37.3.161

    authors: Houlston RS,Tomlinson IP

    更新日期:2000-03-01 00:00:00

  • Mutation screening of MSH2 and MLH1 mRNA in hereditary non-polyposis colon cancer syndrome.

    abstract::Germline mutations in four human mismatch repair genes (MSH2, MLH1, PMS1, and PMS2) have been reported to cause hereditary non-polyposis colon cancer syndrome (HNPCC). The identification of germline mutations in HNPCC kindreds allows precise diagnosis and accurate predictive testing. To investigate further the genetic...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.33.9.726

    authors: Froggatt NJ,Brassett C,Koch DJ,Evans DG,Hodgson SV,Ponder BA,Maher ER

    更新日期:1996-09-01 00:00:00

  • Identification of novel MUNC13-4 mutations in familial haemophagocytic lymphohistiocytosis and functional analysis of MUNC13-4-deficient cytotoxic T lymphocytes.

    abstract:BACKGROUND:Familial haemophagocytic lymphohistiocytosis (FHL) has an autosomal recessive mode of inheritance and consists of at least three subtypes. FHL2 subtype with perforin (PRF1) mutation accounts for 30% of all FHL cases, while FHL with MUNC13-4 mutation was recently identified and designated as FHL3 subtype. OB...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.2004.021121

    authors: Yamamoto K,Ishii E,Sako M,Ohga S,Furuno K,Suzuki N,Ueda I,Imayoshi M,Yamamoto S,Morimoto A,Takada H,Hara T,Imashuku S,Sasazuki T,Yasukawa M

    更新日期:2004-10-01 00:00:00

  • Impaired HLA capping capacity of peripheral blood lymphocytes in Duchenne muscular dystrophy.

    abstract::The cap capacity in nine Duchenne muscular dystrophy (DMD) patients and in 23 healthy male subjects (14 adults and nine neonates) has been investigated by inducing capping of HLA molecules. The evaluation of capping percentages ranged in healthy controls from 44 to 61 with a mean value of 53.39 +/- 4.89, while DMD pat...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.21.3.182

    authors: Sensi A,Venturoli A,Traniello S,Lucci M,Vullo C,Conighi C,Mattiuz PL,Båricordi OR

    更新日期:1984-06-01 00:00:00

  • Recurrence risks in complex inheritance with special regard to pyloric stenosis.

    abstract::A large body of data on segregating families is used to generate specific recurrence risks conditional on sex and birth order for the best-fitting model of polygenes plus maternal effect. The method is general for diseases of complex inheritance, and lies within the competence of any serious genetic clinic. The questi...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.14.6.408

    authors: Lalouel JM,Morton NE,MacLean CJ,Jackson J

    更新日期:1977-12-01 00:00:00

  • Gender-stratified analysis of DLG5 R30Q in 4707 patients with Crohn disease and 4973 controls from 12 Caucasian cohorts.

    abstract:BACKGROUND:DLG5 p.R30Q has been reported to be associated with Crohn disease (CD), but this association has not been replicated in most studies. A recent analysis of gender-stratified data from two case-control studies and two population cohorts found an association of DLG5 30Q with increased risk of CD in men but not ...

    journal_title:Journal of medical genetics

    pub_type: 信件

    doi:10.1136/jmg.2007.050773

    authors: Browning BL,Annese V,Barclay ML,Bingham SA,Brand S,Büning C,Castro M,Cucchiara S,Dallapiccola B,Drummond H,Ferguson LR,Ferraris A,Fisher SA,Gearry RB,Glas J,Henckaerts L,Huebner C,Knafelz D,Lakatos L,Lakatos PL,La

    更新日期:2008-01-01 00:00:00

  • Dilemmas in counselling: the EEC syndrome.

    abstract::A family with the EEC syndrome is reported. Two sibs have the classical form of the condition with ectrodactyly, ectodermal dysplasia, and clefting. Their mother, however, has only minimal evidence, with preaxial polydactyly of the right hand and duplication of the terminal phalanx of the second toe of the left foot w...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.27.12.752

    authors: Tse K,Temple IK,Baraitser M

    更新日期:1990-12-01 00:00:00

  • Epigenetic state and expression of imprinted genes in umbilical cord correlates with growth parameters in human pregnancy.

    abstract:BACKGROUND:Genomic imprinting is a process causing genes to be expressed according to parental origin. Imprinting acts to coordinate fetal and prenatal growth, as well as control postnatal adaptations. Studies on human imprinting are confounded by tissue availability, sampling variability and limitations posed by tissu...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmedgenet-2012-100858

    authors: Lim AL,Ng S,Leow SC,Choo R,Ito M,Chan YH,Goh SK,Tng E,Kwek K,Chong YS,Gluckman PD,Ferguson-Smith AC

    更新日期:2012-11-01 00:00:00

  • Prediction of consanguinity using human DNA fingerprints.

    abstract::DNA fingerprinting was performed to verify the pedigree structure of a family under investigation for an unusual case of beta thalassaemia. A higher than expected proportion of hypervariable bands was shared by the proband and his mother, leading to suspicion that the child had been the product of a consanguineous mat...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.25.10.660

    authors: Wells RA,Wonke B,Thein SL

    更新日期:1988-10-01 00:00:00

  • New insights into 5α-reductase type 2 deficiency based on a multi-centre study: regional distribution and genotype-phenotype profiling of SRD5A2 in 190 Chinese patients.

    abstract:BACKGROUND:The 5α-reductase type 2 (5α-RD2) deficiency caused by mutations in the steroid 5α-reductase 2 (SRD5A2) gene results in variable degrees of undervirilisation in patients with 46,XY disorders of sex development. This study aims to profile the regional distribution and phenotype-genotype characteristics of SRD5...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章,多中心研究

    doi:10.1136/jmedgenet-2018-105915

    authors: Gui B,Song Y,Su Z,Luo FH,Chen L,Wang X,Chen R,Yang Y,Wang J,Zhao X,Fan L,Liu X,Wang Y,Chen S,Gong C

    更新日期:2019-10-01 00:00:00

  • Proteinuria in a patient with the diaphragmatic hernia-hypertelorism-myopia-deafness syndrome: further evidence that the facio-oculo-acoustico-renal syndrome represents the same entity.

    abstract::We present a male infant with hypertelorism, severe myopia and sensorineural deafness, diaphragmatic hernia, and proteinuria. This patient combines features of two distinct genetic conditions, the syndrome of diaphragmatic hernia, exomphalos, absent corpus callosum, hypertelorism, myopia, and sensorineural deafness (M...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.35.1.70

    authors: Devriendt K,Standaert L,Van Hole C,Devlieger H,Fryns JP

    更新日期:1998-01-01 00:00:00

  • Cleidocranial dysplasia: clinical and molecular genetics.

    abstract::Cleidocranial dysplasia (CCD) (MIM 119600) is an autosomal dominant skeletal dysplasia characterised by abnormal clavicles, patent sutures and fontanelles, supernumerary teeth, short stature, and a variety of other skeletal changes. The disease gene has been mapped to chromosome 6p21 within a region containing CBFA1, ...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章,评审

    doi:

    authors: Mundlos S

    更新日期:1999-03-01 00:00:00

  • Adenosine deaminase polymorphism. Associations at clinical level suggest a role in cell functions and immune reactions.

    abstract::It is well known that subjects homozygous for a rare silent allele of ADA may experience a severe combined immunodeficiency. By analogy we have investigated the possible relationship of normal ADA polymorphism with some situations, such as reproductive defects and fetomaternal interactions, in which immunological mech...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.18.5.331

    authors: Bottini E,Carapella E,Cataldi L,Nicotra M,Lucarelli P,Lucarini N,Pascone R,Gloria-Bottini F

    更新日期:1981-10-01 00:00:00

  • Congenital heart defects and left ventricular non-compaction in males with loss-of-function variants in NONO.

    abstract:BACKGROUND:The non-POU domain containing octamer-binding gene (NONO) is located on chromosome Xq13.1 and encodes a member of a small family of RNA-binding and DNA-binding proteins that perform a variety of tasks involved in RNA synthesis, transcriptional regulation and DNA repair. Loss-of-function variants in NONO have...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmedgenet-2016-104039

    authors: Scott DA,Hernandez-Garcia A,Azamian MS,Jordan VK,Kim BJ,Starkovich M,Zhang J,Wong LJ,Darilek SA,Breman AM,Yang Y,Lupski JR,Jiwani AK,Das B,Lalani SR,Iglesias AD,Rosenfeld JA,Xia F

    更新日期:2017-01-01 00:00:00

  • Family in which Duchenne's muscular dystrophy and protan colour blindness are segregating.

    abstract::A family is recorded in which Duchenne's muscular dystrophy and protan colour blindness are segregating. Of 4 members of the second generation at least one is a recombinant. The lod scores have been calculated and added to those already published. ...

    journal_title:Journal of medical genetics

    pub_type: 杂志文章

    doi:10.1136/jmg.14.2.130

    authors: Greig DN

    更新日期:1977-04-01 00:00:00