Advanced search
Publication Cover
Expert Review of Molecular Diagnostics Volume 12, 2012 - Issue 1
Submit an article Journal homepage
115
Views
14
CrossRef citations to date
0
Altmetric
Perspective

How novel molecular diagnostic technologies and biomarkers are revolutionizing genetic testing and patient care

Linnea M Baudhuin Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA;[email protected]
,
Leslie J Donato Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
&
Timothy S Uphoff Molecular Pathology Laboratory, Marshfield Laboratories, Marshfield Clinic, 1000 N Oak St, Marshfield, WI 54449, USA
Pages 25-37 | Published online: 09 Jan 2014

References

  • Delfino KR, Serão NVL, Southey BR, Rodriguez-Zas SL. Therapy-, gender- and race-specific microRNA markers, target genes and networks related to glioblastoma recurrence and survival. Cancer Genomics Proteomics8(4), 173–183 (2011).
  • Ha TY. MicroRNAs in human diseases: from cancer to cardiovascular disease. Immune Netw.11(3), 135–154 (2011).
  • Venter JC, Adams MD, Myers EW et al. The sequence of the human genome. Science291(5507), 1304–1351 (2001).
  • McPherson JD, Marra M, Hillier L et al. A physical map of the human genome. Nature409(6822), 934–941 (2001).
  • Metzker ML. Sequencing technologies – the next generation. Nat. Rev. Genet.11(1), 31–46 (2010).
  • Cullum R, Alder O, Hoodless PA. The next generation: using new sequencing technologies to analyse gene regulation. Respirology16(2), 210–222 (2011).
  • Maher CA, Kumar-Sinha C, Cao X et al. Transcriptome sequencing to detect gene fusions in cancer. Nature458(7234), 97–101 (2009).
  • Dressman D, Yan H, Traverso G, Kinzler KW, Vogelstein B. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc. Natl Acad. Sci. USA100(15), 8817–8822 (2003).
  • Fedurco M, Romieu A, Williams S, Lawrence I, Turcatti G. BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res.34(3), e22 (2006).
  • Braslavsky I, Hebert B, Kartalov E, Quake SR. Sequence information can be obtained from single DNA molecules. Proc. Natl Acad. Sci. USA100(7), 3960–3964 (2003).
  • Ng SB, Bigham AW, Buckingham KJ et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat. Genet.42(9), 790–793 (2010).
  • Ng SB, Buckingham KJ, Lee C et al. Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet.42(1), 30–35 (2010).
  • Lupski JR, Reid JG, Gonzaga-Jauregui C et al. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N. Engl. J. Med.362(13), 1181–1191 (2010).
  • Regalado ES, Guo DC, Villamizar C et al. Exome sequencing identifies SMAD3 mutations as a cause of familial thoracic aortic aneurysm and dissection with intracranial and other arterial aneurysms. Circ. Res.109(6), 680–686 (2011).
  • Galmiche L, Serre V, Beinat M et al. Exome sequencing identifies MRPL3 mutation in mitochondrial cardiomyopathy. Hum. Mut.32(11), 1225–1231 (2011).
  • Comino-Mendez I, Gracia-Aznarez FJ, Schiavi F et al. Exome sequencing identifies MAX mutations as a cause of hereditary pheochromocytoma. Nat. Genet.43(7), 663–667 (2011).
  • Hershberger RE, Siegfried JD. Update 2011: clinical and genetic issues in familial dilated cardiomyopathy. J. Am. Coll. Card.57(16), 1641–1649 (2011).
  • Shendure J, Ji H. Next-generation DNA sequencing. Nat. Biotech.26(10), 1135–1145 (2008).
  • Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res.36(16), e105 (2008).
  • Su Z, Ning B, Fang H et al. Next-generation sequencing and its applications in molecular diagnostics. Expert Rev. Mol. Diagn.11(3), 333–343 (2011).
  • Natrajan R, Reis-Filho JS. Next-generation sequencing applied to molecular diagnostics. Expert Rev. Mol. Diagn.11(4), 425–444 (2011).
  • Pop M, Salzberg SL. Bioinformatics challenges of new sequencing technology. Trends Genet.24(3), 142–149 (2008).
  • Trapnell C, Salzberg SL. How to map billions of short reads onto genomes. Nat. Biotech.27(5), 455–457 (2009).
  • Koboldt DC, Ding L, Mardis ER, Wilson RK. Challenges of sequencing human genomes. Briefings Bioinform.11(5), 484–498 (2010).
  • Schadt EE, Turner S, Kasarskis A. A window into third-generation sequencing. Hum. Mol. Genet.19(R2), R227–R240 (2010).
  • Raffan E, Semple RK. Next generation sequencing – implications for clinical practice. Br. Med. Bull.99, 53–71 (2011).
  • Ajay SS, Parker SC, Ozel Abaan H, Fuentes Fajardo KV, Margulies EH. Accurate and comprehensive sequencing of personal genomes. Genom. Res.21(9), 1498–1505 (2011).
  • 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature467(7319), 1061–1073 (2010).
  • Pennisi E. Genomics. 1000 genomes project gives new map of genetic diversity. Science330(6004), 574–575 (2010).
  • Kingsmore SF, Saunders CJ. Deep sequencing of patient genomes for disease diagnosis: when will it become routine? Sci. Transl. Med.3(87), 87ps23 (2011).
  • Kohonen-Corish MR, Al-Aama JY, Auerbach AD et al. How to catch all those mutations – the report of the third human variome project meeting, UNESCO Paris. Hum. Mut.31(12), 1374–1381 (2010).
  • Richards CS, Bale S, Bellissimo DB et al. ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007. Genet. Med.10(4), 294–300 (2008).
  • Bell CJ, Dinwiddie DL, Miller NA et al. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci. Transl. Med.3(65), 65ra64 (2011).
  • Trask BJ. Fluorescence in situ hybridization: applications in cytogenetics and gene mapping. Trends Genet.7(5), 149–154 (1991).
  • Shaffer LG, Kennedy GM, Spikes AS, Lupski JR. Diagnosis of CMT1A duplications and HNPP deletions by interphase FISH: implications for testing in the cytogenetics laboratory. Am. J. Hum. Gen.69(3), 325–331 (1997).
  • ten Bosch JR, Grody WW. Keeping up with the next generation: massively parallel sequencing in clinical diagnostics. J Mol. Diagn.10(6), 484–492 (2008).
  • Talkowski ME, Ernst C, Heilbut A et al. Next-generation sequencing strategies enable routine detection of balanced chromosome rearrangements for clinical diagnostics and genetic research. Am. J. Hum. Genet.88(4), 469–481 (2011).
  • Regier DA, Friedman JM, Marra CA. Value for money? Array genomic hybridization for diagnostic testing for genetic causes of intellectual disability. Am. J. Hum. Genet.86(5), 765–772 (2010).
  • Bejjani BA, Shaffer LG. Clinical utility of contemporary molecular cytogenetics. Ann. Rev. Genom. Hum. Genet.9, 71–86 (2008).
  • Manning M, Hudgins L. Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genet. Med.12(11), 742–745 (2010).
  • Oostlander AE, Meijer GA, Ylstra B. Microarray-based comparative genomic hybridization and its applications in human genetics. Clin. Genet.66(6), 488–495 (2004).
  • Snijders AM, Nowak N, Segraves R et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat. Genet.29(3), 263–264 (2001).
  • Miller DT, Adam MP, Aradhya S et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am. J. Hum. Gen.86(5), 749–764 (2010).
  • Friedman JM, Baross A, Delaney AD et al. Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am. J. Hum. Gen.79(3), 500–513 (2006).
  • Vermeesch JR, Fiegler H, de Leeuw N et al. Guidelines for molecular karyotyping in constitutional genetic diagnosis. Eur. J. Hum. Genet.15(11), 1105–1114 (2007).
  • Fan YS, Jayakar P, Zhu H et al. Detection of pathogenic gene copy number variations in patients with mental retardation by genomewide oligonucleotide array comparative genomic hybridization. Hum. Mut.28(11), 1124–1132 (2007).
  • Tester DJ, Benton AJ, Train L, Deal B, Baudhuin LM, Ackerman MJ. Prevalence and spectrum of large deletions or duplications in the major long QT syndrome-susceptibility genes and implications for long QT syndrome genetic testing. Am. J. Cardiol.106(8), 1124–1128 (2010).
  • Barc J, Briec F, Schmitt S et al. Screening for copy number variation in genes associated with the long QT syndrome: clinical relevance. J. Am. Coll. Cardiol.57(1), 40–47 (2011).
  • Tyson C, Harvard C, Locker R et al. Submicroscopic deletions and duplications in individuals with intellectual disability detected by array-CGH. Am. J. Med. Genet. A139(3), 173–185 (2005).
  • Beaudet AL. Ethical issues raised by common copy number variants and single nucleotide polymorphisms of certain and uncertain significance in general medical practice. Genome Med.2(7), 42 (2010).
  • Lo YM, Corbetta N, Chamberlain PF et al. Presence of fetal DNA in maternal plasma and serum. Lancet350(9076), 485–487 (1997).
  • Beaudet AL. Progress toward noninvasive prenatal diagnosis. Clin. Chem.57(6), 802–804 (2011).
  • Lo YM, Tein MS, Lau TK et al. Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis. Am. J. Hum. Genet.62(4), 768–775 (1998).
  • Lo YM, Hjelm NM, Fidler C et al. Prenatal diagnosis of fetal RHD status by molecular analysis of maternal plasma. N. Engl. J. Med.339(24), 1734–1738 (1998).
  • Van der Schoot CE, Soussan AA, Koelewijn J, Bonsel G, Paget-Christiaens LG, de Haas M. Non-invasive antenatal RHD typing. Transfus. Clin. Biol.13(1–2), 53–57 (2006).
  • Daniels G, Finning K, Martin P, Massey E. Noninvasive prenatal diagnosis of fetal blood group phenotypes: current practice and future prospects. Prenat. Diagn.29(2), 101–107 (2009).
  • Daniels G, van der Schoot CE, Gassner C, Olsson ML. Report of the third international workshop on molecular blood group genotyping. Vox Sang.96(4), 337–343 (2009).
  • Scheffer P, van der Schoot C, Page-Christiaens G, de Haas M. Noninvasive fetal blood group genotyping of rhesus D, C, E and of K in alloimmunised pregnant women: evaluation of a 7-year clinical experience. BJOG118(11), 1340–1348 (2011).
  • Scheffer PG, van der Schoot CE, Page-Christiaens GC, Bossers B, van Erp F, de Haas M. Reliability of fetal sex determination using maternal plasma. Obstet. Gynecol.115(1), 117–126 (2010).
  • Malone FD, Canick JA, Ball RH et al. First-trimester or second-trimester screening, or both, for Down’s syndrome. N. Engl. J. Med.353(19), 2001–2011 (2005).
  • Chiu RW, Akolekar R, Zheng YW et al. Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ342, c7401 (2011).
  • Papageorgiou EA, Karagrigoriou A, Tsaliki E, Velissariou V, Carter NP, Patsalis PC. Fetal-specific DNA methylation ratio permits noninvasive prenatal diagnosis of trisomy 21. Nat. Med.17(4), 510–513 (2011).
  • Tong YK, Ding C, Chiu RW et al. Noninvasive prenatal detection of fetal trisomy 18 by epigenetic allelic ratio analysis in maternal plasma: theoretical and empirical considerations. Clin. Chem.52(12), 2194–2202 (2006).
  • Li Y, Zimmermann B, Rusterholz C, Kang A, Holzgreve W, Hahn S. Size separation of circulatory DNA in maternal plasma permits ready detection of fetal DNA polymorphisms. Clin. Chem.50(6), 1002–1011 (2004).
  • Li Y, Di Naro E, Vitucci A, Zimmermann B, Holzgreve W, Hahn S. Detection of paternally inherited fetal point mutations for β-thalassemia using size-fractionated cell-free DNA in maternal plasma. JAMA293(7), 843–849 (2005).
  • Li Y, Holzgreve W, Page-Christiaens GC, Gille JJ, Hahn S. Improved prenatal detection of a fetal point mutation for achondroplasia by the use of size-fractionated circulatory DNA in maternal plasma – case report. Prenat. Diag.24(11), 896–898 (2004).
  • Liao GJ, Lun FM, Zheng YW et al. Targeted massively parallel sequencing of maternal plasma DNA permits efficient and unbiased detection of fetal alleles. Clin. Chem.57(1), 92–101 (2011).
  • Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell75(5), 843–854 (1993).
  • Nozawa M, Miura S, Nei M. Origins and evolution of microRNA genes in Drosophila species. Genome Biol. Evol.2, 180–189 (2010).
  • Ach RA, Wang H, Curry B. Measuring microRNAs: comparisons of microarray and quantitative PCR measurements, and of different total RNA prep methods. BMC Biotechnol.8, 69 (2008).
  • Chapin SC, Doyle PS. Ultrasensitive multiplexed microRNA quantification on encoded gel microparticles using rolling circle amplification. Analyt. Chem.83(18), 7179–7185 (2011).
  • Jiang Q, Wang Y, Hao Y et al. miR2 disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res.37(Suppl. 1), D98–D104 (2009).
  • Prosser HM, Koike-Yusa H, Cooper JD, Law FC, Bradley A. A resource of vectors and ES cells for targeted deletion of microRNAs in mice. Nat. Biotechnol.29(9), 840–845 (2011).
  • Ramsingh G, Koboldt DC, Trissal M et al. Complete characterization of the microRNAome in a patient with acute myeloid leukemia. Blood116(24), 5316–5326 (2010).
  • Zhang Y, Li M, Wang H et al. Profiling of 95 microRNAs in pancreatic cancer cell lines and surgical specimens by real-time PCR analysis. World J. Surg.33(4), 698–709 (2009).
  • Rosenwald S, Gilad S, Benjamin S et al. Validation of a microRNA-based qRT-PCR test for accurate identification of tumor tissue origin. Mod. Pathol.23(6), 814–823 (2010).
  • Pillai R, Deeter R, Rigl CT et al. Validation and reproducibility of a microarray-based gene expression test for tumor identification in formalin-fixed, paraffin-embedded specimens. J. Mol. Diagn.13(1), 48–56 (2011).
  • Megiorni F, Pizzuti A, Frati L. Clinical significance of microRNA expression profiles and polymorphisms in lung cancer development and management. Pathol. Res. Int.2011, 780652 (2011).
  • Sozzi G, Pastorino U, Croce CM. MicroRNAs and lung cancer: from markers to targets. Cell Cycle10(13), 2045–1046 (2011).
  • Bianchi F, Nicassio F, Marzi M et al. A serum circulating miRNA diagnostic test to identify asymptomatic high-risk individuals with early stage lung cancer. EMBO Mol. Med.3(8), 495–503 (2011).
  • Small EM, Frost RJA, Olson EN. MicroRNAs add a new dimension to cardiovascular disease. Circulation121(8), 1022–1032 (2010).
  • Maes OC, Chertkow HM, Wang E, Schipper HM. MicroRNA: implications for Alzheimer disease and other human CNS disorders. Curr. Genomics10(3), 154–168 (2009).
  • Alisi A, Da Sacco L, Bruscalupi G et al. Mirnome analysis reveals novel molecular determinants in the pathogenesis of diet-induced nonalcoholic fatty liver disease. Lab. Invest.91(2), 283–293 (2011).
  • Wang DZ. MicroRNAs in cardiac development and remodeling. Pediatr. Cardiol.31(3), 357–362 (2010).
  • Wang N, Zhou Z, Liao X, Zhang T. Role of microRNAs in cardiac hypertrophy and heart failure. IUBMB Life61(6), 566–571 (2009).
  • Ono K, Kuwabara Y, Han J. MicroRNAs and cardiovascular diseases. FEBS J.278(10), 1619–1633 (2011).
  • McDonald JS, Milosevic D, Reddi HV, Grebe SK, Algeciras-Schimnich A. Analysis of circulating microRNA: preanalytical and analytical challenges. Clin. Chem.57(6), 833–840 (2011).
  • Dimou A, Harrington K, Syrigos KN. From the bench to bedside: biological and methodology considerations for the future of companion diagnostics in nonsmall cell lung cancer. Pathol. Res. Int.2011, 312346 (2011).
  • La Thangue NB, Kerr DJ. Predictive biomarkers: a paradigm shift towards personalized cancer medicine. Nat. Rev.8(10), 587–596 (2011).
  • Ross JS. Cancer biomarkers, companion diagnostics and personalized oncology. Biomark. Med.5(3), 277–279 (2011).
  • Hamburg MA, Collins FS. The path to personalized medicine. N. Engl. J. Med.363(4), 301–304 (2010).
  • Bosworth HB, Granger BB, Mendys P et al. Medication adherence: a call for action. Am. Heart J.162(3), 412–424 (2011).
  • Tucker G. Pharmacogenetics – expectations and reality. BMJ329(7456), 4–6 (2004).
  • Evans JP, Meslin EM, Marteau TM, Caulfield T. Genomics: deflating the genomic bubble. Science331(6019), 861–862 (2011).
  • Jensen K, Murray F. Intellectual property. Enhanced: intellectual property landscape of the human genome. Science310(5746), 239–240 (2005).
  • Baudhuin LM. Determining the optimal approach for government-regulated genetic testing. Clin. Chem.57(1), 7–8 (2011).
  • Gibbs JN. Regulating molecular diagnostic assays: developing a new regulatory structure for a new technology. Expert Rev. Mol. Diagn.11(4), 367–381 (2011).
  • Beaudet AL. Which way for genetic-test regulation? Leave test interpretation to specialists. Nature466(7308), 816–817 (2010).
  • Javitt G. Which way for genetic-test regulation? Assign regulation appropriate to the level of risk. Nature466(7308), 817–818 (2010).
  • Chiang DY, Getz G, Jaffe DB et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Method.6(1), 99–103 (2009).
  • Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet.11(10), 685–696 (2011).
  • Ku CS, Naidoo N, Wu M, Soong R. Studying the epigenome using next generation sequencing. J. Med. Gen.48(11), 721–730 (2011).
  • Campbell PJ, Stephens PJ, Pleasance ED et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet.40(6), 722–729 (2008).
  • Hoggatt J. Personalized medicine – trends in molecular diagnostics: exponential growth expected in the next ten years. Mol. Diagn. Ther.15(1), 53–55 (2011).
  • Li C. Personalized medicine – the promised land: are we there yet? Clin. Genet.79(5), 403–412 (2011).

Websites

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.