Advertisement

Diagnostic Revolution Post-Human Genome Sequence Project: High-Throughput Technologies and Bioinformatics

  • Noor Ahmad Shaik
  • Babajan Banaganapalli
  • Jumana Y. Al-Aama
  • Ramu ElangoEmail author
Chapter
  • 736 Downloads

Abstract

Diagnostic techniques, after the completion of Human Genome Sequencing Project, have evolved with next-generation sequencing. This revolution has changed the diagnostics landscape with a variety of kits and methods available for the patients. This equipped the clinical management team with powerful tools in providing better service and reducing or delaying devastating disease effects on the patient as well as providing better opportunities with preventive efforts of many diseases.

Keywords

Mutation Sequencing Exome sequencing Microarray Human Genome National genome projects Genetic diagnosis Single gene disease 

References

  1. Alrayes N, Mohamoud HS, Ahmed S, Almramhi MM, Shuaib TM, Wang J, Al-Aama JY, Everett K, Nasir J, Jelani M (2016) The alkylglycerol monooxygenase (AGMO) gene previously involved in autism also causes a novel syndromic form of primary microcephaly in a consanguineous Saudi family. J Neurol Sci 15/363:240–244CrossRefGoogle Scholar
  2. Altschul S, Gish W, Miller W, Myers E, Lipman D (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410.  https://doi.org/10.1016/S0022-2836(05)80360-2. PMID 2231712CrossRefPubMedPubMedCentralGoogle Scholar
  3. Barwell JG, O’Sullivan RBG, Mansbridge LK, Lowry JM, Dorkins HR (2018) Challenges in implementing genomic medicine: the 100,000 genomes project. J Transl Genet Genom 2:13.  https://doi.org/10.20517/jtgg.2018.17CrossRefGoogle Scholar
  4. Bycroft C, Freeman C, Petkova D, Band G, Elliott LT, Sharp K, Motyer A, Vukcevic D, Delaneau O, O’Connell J, Cortes A, Welsh S, Young A, Effingham M, McVean G, Leslie S, Allen N, Donnelly P, Marchini J (2018) The UK Biobank resource with deep phenotyping and genomic data. Nature 562(7726):203–209.  https://doi.org/10.1038/s41586-018-0579-zCrossRefPubMedPubMedCentralGoogle Scholar
  5. Deciphering Developmental Disorders Study -265 collaborators (2015) Large-scale discovery of novel genetic causes of developmental disorders. Nature 519(7542):223–228.  https://doi.org/10.1038/nature14135CrossRefGoogle Scholar
  6. Elliott LT, Sharp K, Alfaro-Almagro F, Shi S, Miller KL, Douaud G, Marchini J, Smith SM (2018) Genome-wide association studies of brain imaging phenotypes in UK Biobank. Nature 562(7726):210–216.  https://doi.org/10.1038/s41586-018-0571-7. Epub 2018 Oct 10CrossRefPubMedPubMedCentralGoogle Scholar
  7. Firth HV, Richards SM, Paul Bevan AP, Clayton S, CorpasM RD, Van Vooren S, Moreau Y, Pettett RM, Carter NP (2009) DECIPHER: database of chromosomal imbalance and phenotype in humans using ensembl resources. Am J Hum Genet 84:524–533CrossRefGoogle Scholar
  8. Gräf S, Haimel M, Bleda B, Hadinnapola C, Southgate L, Li W, Hodgson J, Liu B, Salmon RM, Southwood M, Machado RD, Martin JM, Treacy CM, Yates K, Daugherty LC, Shamardina O, Whitehorn D, Holden S, Aldred M, Bogaard HJ, Church C, Coghlan G, Condliffe R, Corris PA, Danesino C, Eyries M, Gall H, Ghio S, Ghofrani HA, JSR G, Girerd B, Houweling AC, Howard L, Humbert M, Kiely DG, Kovacs G, RV MKR, Moledina S, Montani D, Newnham M, Olschewski A, Olschewski H, Peacock AJ, Pepke-Zaba J, Prokopenko I, Rhodes CJ, Scelsi L, Seeger W, Soubrier F, Stein DF, Suntharalingam J, Swietlik EM, Toshner MR, van Heel DA, Vonk Noordegraaf A, Waisfisz Q, Wharton J, Wort SJ, Ouwehand WH, Soranzo N, Lawrie A, Upton PD, Wilkins MR, Trembeth RC, Morrell NW (2018) Identification of rare sequence variation underlying heritable pulmonary arterial hypertension. Nat Commun 9:1416.  https://doi.org/10.1038/s41467-018-03672-4CrossRefPubMedPubMedCentralGoogle Scholar
  9. Grant M, Maytum JP (2018) What will follow the first hundred thousand genomes in the NHS? Per Med 15(4):239–241.  https://doi.org/10.2217/pme-2018-0025CrossRefPubMedGoogle Scholar
  10. Gusella JF, Wexler NS, Conneally PM, Naylor SL, Anderson MA, Tanzi RE, Watkins PC, Ottina K, Wallace MR, Sakaguchi AY, Young AB, Shoulson I, Bonilla E, Martin JB (1983) A polymorphic DNA marker genetically linked to Huntington’s disease. Nature 306(5940):234–238CrossRefGoogle Scholar
  11. Haas ME, Aragam KG, Emdin CA, Bick AG, International Consortium for Blood Pressure, Hemani G, Davey Smith G, Kathiresan S (2018) Genetic Association of Albuminuria with cardiometabolic disease and blood pressure. Am J Hum Genet 103(4):461–473.  https://doi.org/10.1016/j.ajhg.2018.08.004. Epub 2018 Sep 13CrossRefPubMedPubMedCentralGoogle Scholar
  12. Inouye M, Abraham G, Nelson CP, Wood AM, Sweeting MJ, Dudbridge F, Lai FY, Kaptoge S, Brozynska M, Wang T, Ye S, Webb TR, Rutter MK, Tzoulaki I, Patel RS, Loos RJF, Keavney B, Hemingway H, Thompson J, Watkins H, Deloukas P, Di Angelantonio E, Butterworth AS, Danesh J, Samani NJ, UK Biobank CardioMetabolic Consortium CHD Working Group (2018) Genomic risk prediction of coronary artery disease in 480,000 adults: implications for primary prevention. J Am Coll Cardiol 72(16):1883–1893.  https://doi.org/10.1016/j.jacc.2018.07.079CrossRefPubMedPubMedCentralGoogle Scholar
  13. Klarin D, Damrauer SM, Cho K, Sun YV, Teslovich TM, Honerlaw J, Gagnon DR, DuVall SL, Li J, Peloso GM, Chaffin M, Small AM, Huang J, Tang H, Lynch JA, Ho YL, Liu DJ, Emdin CA, Li AH, Huffman JE, Lee JS, Natarajan P, Chowdhury R, Saleheen D, Vujkovic M, Baras A, Pyarajan S, Di Angelantonio E, Neale BM, Naheed A, Khera AV, Danesh J, Chang KM, Abecasis G, Willer C, Dewey FE, Carey DJ, Global Lipids Genetics Consortium, Myocardial Infarction Genetics (MIGen) Consortium, Geisinger-Regeneron DiscovEHR Collaboration, VA Million Veteran Program, Concato J, Gaziano JM, O’Donnell CJ, Tsao PS, Kathiresan S, Rader DJ, Wilson PWF, Assimes TL (2018) Genetics of blood lipids among ~300,000 multi-ethnic participants of the Million Veteran Program. Nat Genet 50(11):1514–1523.  https://doi.org/10.1038/s41588-018-0222-9CrossRefPubMedPubMedCentralGoogle Scholar
  14. Klintman J, Barmpouti K, Knight SJL, Robbe P, Dreau H, Clifford R, Ridout K, Burns A, Timbs A, Bruce D, Antoniou P, Sosinsky A, Becq J, Bentley D, Hillmen P, Taylor JC, Caulfield M, Schuh AH (2018) Clinical-grade validation of whole genome sequencing reveals robust detection of low-frequency variants and copy number alterations in CLL. Br J Haematol 182:412–417.  https://doi.org/10.1111/bjh.15406CrossRefPubMedGoogle Scholar
  15. Lipman DJ, Pearson WR (1985) Rapid and sensitive protein similarity searches. Science 227(4693):1435–1441.  https://doi.org/10.1126/science.2983426. PMID 2983426CrossRefGoogle Scholar
  16. Mohamoud HS, Ahmed S, Jelani M, Alrayes N, Childs K, Vadgama N, Almramhi MM, Al-Aama JY, Goodbourn S, Nasir J (2018) A missense mutation in TRAPPC6A leads to build-up of the protein, in patients with a neurodevelopmental syndrome and dysmorphic features. Sci Rep 8(1):2053.  https://doi.org/10.1038/s41598-018-20658-wCrossRefPubMedPubMedCentralGoogle Scholar
  17. Monies D, Abouelhoda M, AlSayed M, Alhassnan Z, Alotaibi M, Kayyali H, Al-Owain M, Shah A, Rahbeeni Z, Al-Muhaizea MA, Alzaidan HI, Cupler E, Bohlega S, Faqeih E, Faden M, Alyounes B, Jaroudi D, Goljan E, Elbardisy H, Akilan A, Albar R, Aldhalaan H, Gulab S, Chedrawi A, Al Saud BK, Kurdi W, Makhseed N, Alqasim T, El Khashab HY, Al-Mousa H, Alhashem A, Kanaan I, Algoufi T, Alsaleem K, Basha TA, Al-Murshedi F, Khan S, Al-Kindy A, Alnemer M, Al-Hajjar S, Alyamani S, Aldhekri H, Al-Mehaidib A, Arnaout R, Dabbagh O, Shagrani M, Broering D, Tulbah M, Alqassmi A, Almugbel M, AlQuaiz M, Alsaman A, Al-Thihli K, Sulaiman RA, Al-Dekhail W, Alsaegh A, Bashiri FA, Qari A, Alhomadi S, Alkuraya H, Alsebayel M, Hamad MH, Szonyi L, Abaalkhail F, Al-Mayouf SM, Almojalli H, Alqadi KS, Elsiesy H, Shuaib TM, Seidahmed MZ, Abosoudah I, Akleh H, AlGhonaium A, Alkharfy TM, Al Mutairi F, Eyaid W, Alshanbary A, Sheikh FR, Alsohaibani FI, Alsonbul A, Al Tala S, Balkhy S, Bassiouni R, Alenizi AS, Hussein MH, Hassan S, Khalil M, Tabarki B, Alshahwan S, Oshi A, Sabr Y, Alsaadoun S, Salih MA, Mohamed S, Sultana H, Tamim A, El-Haj M, Alshahrani S, Bubshait DK, Alfadhel M, Faquih T, El-Kalioby M, Subhani S, Shah Z, Moghrabi N, Meyer BF, Alkuraya FS (2017) The landscape of genetic diseases in Saudi Arabia based on the first 1000 diagnostic panels and exomes. Hum Genet 136(8):921–939.  https://doi.org/10.1007/s00439-017-1821-8CrossRefPubMedPubMedCentralGoogle Scholar
  18. Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85(8):2444–2448.  https://doi.org/10.1073/pnas.85.8.2444CrossRefPubMedPubMedCentralGoogle Scholar
  19. Pennarun G, Escudier E, Chapelin C, Bridoux A-M, Cacheux V, Roger G, Clément A, Goossens M, Amselem S, Duriez B (1999) Loss-of-function mutations in a human gene related to Chlamydomonas reinhardtii dynein IC78 result in primary ciliary dyskinesia. Am J Hum Genet 65:1508–1519.  https://doi.org/10.1086/302683CrossRefPubMedPubMedCentralGoogle Scholar
  20. Reynolds JJ, Bicknell LS, Carroll P, Higgs MR, Shaheen R, Murray JE, Papadopoulos DK, Leitch A, Murina O, Tarnauskaitė Ž, Wessel SR, Zlatanou A, Vernet A, von Kriegsheim A, Mottram RM, Logan CV, Bye H, Li Y, Brean A, Maddirevula S, Challis RC, Skouloudaki K, Almoisheer A, Alsaif HS, Amar A, Prescott NJ, Bober MB, Duker A, Faqeih E, Seidahmed MZ, Al Tala S, Alswaid A, Ahmed S, Al-Aama JY, Altmüller J, Al Balwi M, Brady AF, Chessa L, Cox H, Fischetto R, Heller R, Henderson BD, Hobson E, Nürnberg P, Percin EF, Peron A, Spaccini L, Quigley AJ, Thakur S, Wise CA, Yoon G, Alnemer M, Tomancak P, Yigit G, Taylor AM, Reijns MA, Simpson MA, Cortez D, Alkuraya FS, Mathew CG, Jackson AP, Stewart GS (2017) Mutations in DONSON disrupt replication fork stability and cause microcephalic dwarfism. Nat Genet 49(4):537–549.  https://doi.org/10.1038/ng.3790CrossRefPubMedPubMedCentralGoogle Scholar
  21. Scott EM, Halees A, Itan Y, Spencer EG, He Y, Azab MA, Gabriel SB, Belkadi A, Boisson B, Abel L, Clark AG, Greater Middle East Variome Consortium, Alkuraya FS, Casanova JL, Gleeson JG (2016) Characterization of greater middle eastern genetic variation for enhanced disease gene discovery. Nat Genet 48(9):1071–1076.  https://doi.org/10.1038/ng.3592CrossRefPubMedPubMedCentralGoogle Scholar
  22. Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147:195–197.  https://doi.org/10.1016/0022-2836(81)90087-5. PMID 7265238CrossRefGoogle Scholar
  23. The Huntington’s Disease Collaborative Research Group (1993) A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington’s disease chromosomes. Cell 72(6):971–983.  https://doi.org/10.1016/0092-8674(93)90585-E. PMID 8458085CrossRefGoogle Scholar
  24. Turnbull C, Scott RH, Thomas E, Jones L, Murugaesu N, Pretty FB, Halai D, Baple E, Craig C, Hamblin A, Henderson S, Patch C, O’Neill A, Devereaux A, Smith K, Martin AR, Sosinsky A, McDonagh EM, Sultana R, Mueller M, Smedley D, Toms A, Dinh L, Fowler T, Bale M, Hubbard T, Rendon A, Hill S, Caulfield MJ, 100 000 Genomes Project (2018) The 100 000 Genomes Project: bringing whole genome sequencing to the NHS. BMJ 361:k1687.  https://doi.org/10.1136/bmj.k1687CrossRefPubMedGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Noor Ahmad Shaik
    • 1
  • Babajan Banaganapalli
    • 1
  • Jumana Y. Al-Aama
    • 1
  • Ramu Elango
    • 1
    Email author
  1. 1.Princess Al-Jawhara Center of Excellence in Research of Hereditary DisordersDepartment of Genetic Medicine, Faculty of Medicine, King Abdulaziz UniversityJeddahSaudi Arabia

Personalised recommendations