Applicability of Digital PCR to the Investigation of Pediatric-onset Genetic Disorders

Overview

Journal Biomol Detect Quantif

Date 2016 Dec 20

PMID 27990344

Citations 8

Authors

Matthew E R Butchbach

Affiliations

Soon will be listed here.

Abstract

Early-onset rare diseases have a strong impact on child healthcare even though the incidence of each of these diseases is relatively low. In order to better manage the care of these children, it is imperative to quickly diagnose the molecular bases for these disorders as well as to develop technologies with prognostic potential. Digital PCR (dPCR) is well suited for this role by providing an absolute quantification of the target DNA within a sample. This review illustrates how dPCR can be used to identify genes associated with pediatric-onset disorders, to identify copy number status of important disease-causing genes and variants and to quantify modifier genes. It is also a powerful technology to track changes in genomic biomarkers with disease progression. Based on its capability to accurately and reliably detect genomic alterations with high sensitivity and a large dynamic detection range, dPCR has the potential to become the tool of choice for the verification of pediatric disease-associated mutations identified by next generation sequencing, copy number determination and noninvasive prenatal screening.

Citing Articles

Genomic Copy Number Analysis Using Droplet Digital PCR: A Simple Method with EvaGreen Single-Color Fluorescent Design.

Tamura T, Imaizumi T, Shimojima Yamamoto K, Yamamoto T Methods Mol Biol. 2024; 2794:293-304.

PMID: 38630238 DOI: 10.1007/978-1-0716-3810-1_24.

Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond.

Parkins M, Lee B, Acosta N, Bautista M, Hubert C, Hrudey S Clin Microbiol Rev. 2023; 37(1):e0010322.

PMID: 38095438 PMC: 10938902. DOI: 10.1128/cmr.00103-22.

Nucleic Acid Based Testing (NABing): A Game Changer Technology for Public Health.

Khera H, Mishra R Mol Biotechnol. 2023; 66(9):2168-2200.

PMID: 37695473 DOI: 10.1007/s12033-023-00870-4.

Digital PCR Discriminates between SARS-CoV-2 Omicron Variants and Immune Escape Mutations.

Holland S, Holland L, Smith M, Lee M, Hu J, Lim E Microbiol Spectr. 2023; 11(4):e0525822.

PMID: 37306573 PMC: 10434287. DOI: 10.1128/spectrum.05258-22.

Identification of the Novel Methylated Genes' Signature to Predict Prognosis in INRG High-Risk Neuroblastomas.

Liu Z, Li C J Oncol. 2021; 2021:1615201.

PMID: 34557229 PMC: 8455188. DOI: 10.1155/2021/1615201.

References

Rubben A, Bausch B, Nikkels A . Somatic deletion of the NF1 gene in a neurofibromatosis type 1-associated malignant melanoma demonstrated by digital PCR. Mol Cancer. 2006; 5:36. PMC: 1570477. DOI: 10.1186/1476-4598-5-36. View

Barrett A, McDonnell T, Chan K, Chitty L . Digital PCR analysis of maternal plasma for noninvasive detection of sickle cell anemia. Clin Chem. 2012; 58(6):1026-32. DOI: 10.1373/clinchem.2011.178939. View

Abou Tayoun A, Mason-Suares H, Frisella A, Bowser M, Duffy E, Mahanta L . Targeted Droplet-Digital PCR as a Tool for Novel Deletion Discovery at the DFNB1 Locus. Hum Mutat. 2015; 37(1):119-26. DOI: 10.1002/humu.22912. View

Stieglitz E, Troup C, Gelston L, Haliburton J, Chow E, Yu K . Subclonal mutations in SETBP1 confer a poor prognosis in juvenile myelomonocytic leukemia. Blood. 2014; 125(3):516-24. PMC: 4296011. DOI: 10.1182/blood-2014-09-601690. View

Usher C, Handsaker R, Esko T, Tuke M, Weedon M, Hastie A . Structural forms of the human amylase locus and their relationships to SNPs, haplotypes and obesity. Nat Genet. 2015; 47(8):921-5. PMC: 4712930. DOI: 10.1038/ng.3340. View

Saunders C, Miller N, Soden S, Dinwiddie D, Noll A, Alnadi N . Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med. 2012; 4(154):154ra135. PMC: 4283791. DOI: 10.1126/scitranslmed.3004041. View

Sillence K, Roberts L, Hollands H, Thompson H, Kiernan M, Madgett T . Fetal Sex and RHD Genotyping with Digital PCR Demonstrates Greater Sensitivity than Real-time PCR. Clin Chem. 2015; 61(11):1399-407. DOI: 10.1373/clinchem.2015.239137. View

Usmani-Brown S, Lebastchi J, Steck A, Beam C, Herold K, Ledizet M . Analysis of β-cell death in type 1 diabetes by droplet digital PCR. Endocrinology. 2014; 155(9):3694-8. PMC: 4138562. DOI: 10.1210/en.2014-1150. View

Fan H, Blumenfeld Y, El-Sayed Y, Chueh J, Quake S . Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy. Am J Obstet Gynecol. 2009; 200(5):543.e1-7. PMC: 4117196. DOI: 10.1016/j.ajog.2009.03.002. View

10.

Orhant L, Anselem O, Fradin M, Becker P, Beugnet C, Deburgrave N . Droplet digital PCR combined with minisequencing, a new approach to analyze fetal DNA from maternal blood: application to the non-invasive prenatal diagnosis of achondroplasia. Prenat Diagn. 2016; 36(5):397-406. DOI: 10.1002/pd.4790. View

11.

Vasilev V, Daly A, Thiry A, Petrossians P, Fina F, Rostomyan L . McCune-Albright syndrome: a detailed pathological and genetic analysis of disease effects in an adult patient. J Clin Endocrinol Metab. 2014; 99(10):E2029-38. DOI: 10.1210/jc.2014-1291. View

12.

Lun F, Chiu R, Chan K, Leung T, Lau T, Lo Y . Microfluidics digital PCR reveals a higher than expected fraction of fetal DNA in maternal plasma. Clin Chem. 2008; 54(10):1664-72. DOI: 10.1373/clinchem.2008.111385. View

13.

Lo Y, Chan K, Sun H, Chen E, Jiang P, Lun F . Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci Transl Med. 2010; 2(61):61ra91. DOI: 10.1126/scitranslmed.3001720. View

14.

Hindson C, Chevillet J, Briggs H, Gallichotte E, Ruf I, Hindson B . Absolute quantification by droplet digital PCR versus analog real-time PCR. Nat Methods. 2013; 10(10):1003-5. PMC: 4118677. DOI: 10.1038/nmeth.2633. View

15.

Debrand E, Lykoudi A, Bradshaw E, Allen S . A Non-Invasive Droplet Digital PCR (ddPCR) Assay to Detect Paternal CFTR Mutations in the Cell-Free Fetal DNA (cffDNA) of Three Pregnancies at Risk of Cystic Fibrosis via Compound Heterozygosity. PLoS One. 2015; 10(11):e0142729. PMC: 4641687. DOI: 10.1371/journal.pone.0142729. View

16.

Gu S, Posey J, Yuan B, Carvalho C, Luk H, Erikson K . Mechanisms for the Generation of Two Quadruplications Associated with Split-Hand Malformation. Hum Mutat. 2015; 37(2):160-4. PMC: 4718869. DOI: 10.1002/humu.22929. View

17.

Tsui N, Kadir R, Chan K, Chi C, Mellars G, Tuddenham E . Noninvasive prenatal diagnosis of hemophilia by microfluidics digital PCR analysis of maternal plasma DNA. Blood. 2011; 117(13):3684-91. DOI: 10.1182/blood-2010-10-310789. View

18.

Fujiki K, Shirahige K, Kaur M, Deardorff M, Conlin L, Krantz I . Mosaic ratio quantification of isochromosome 12p in Pallister-Killian syndrome using droplet digital PCR. Mol Genet Genomic Med. 2016; 4(3):257-61. PMC: 4867559. DOI: 10.1002/mgg3.200. View

19.

Corbisier P, Pinheiro L, Mazoua S, Kortekaas A, Chung P, Gerganova T . DNA copy number concentration measured by digital and droplet digital quantitative PCR using certified reference materials. Anal Bioanal Chem. 2015; 407(7):1831-40. PMC: 4336415. DOI: 10.1007/s00216-015-8458-z. View

20.

Hindson B, Ness K, Masquelier D, Belgrader P, Heredia N, Makarewicz A . High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem. 2011; 83(22):8604-10. PMC: 3216358. DOI: 10.1021/ac202028g. View