The landscape of genetic diseases in Saudi Arabia based on the first 1000 diagnostic panels and exomes.

Authors:
Dorota Monies Mohamed Abouelhoda Moeenaldeen AlSayed Zuhair Alhassnan Maha Alotaibi Husam Kayyali Mohammed Al-Owain Ayaz Shah Zuhair Rahbeeni Mohammad A Al-Muhaizea Hamad I Alzaidan Edward Cupler Saeed Bohlega Eissa Faqeih Maha Faden Banan Alyounes Dyala Jaroudi Ewa Goljan Hadeel Elbardisy Asma Akilan Renad Albar Hesham Aldhalaan Shamshad Gulab Aziza Chedrawi Bandar K Al Saud Wesam Kurdi Nawal Makhseed Tahani Alqasim Heba Y El Khashab Hamoud Al-Mousa Amal Alhashem Imaduddin Kanaan Talal Algoufi Khalid Alsaleem Talal A Basha Fathiya Al-Murshedi Sameena Khan Adila Al-Kindy Maha Alnemer Sami Al-Hajjar Suad Alyamani Hasan Aldhekri Ali Al-Mehaidib Rand Arnaout Omar Dabbagh Mohammad Shagrani Dieter Broering Maha Tulbah Amal Alqassmi Maisoon Almugbel Mohammed AlQuaiz Abdulaziz Alsaman Khalid Al-Thihli Raashda A Sulaiman Wajeeh Al-Dekhail Abeer Alsaegh Fahad A Bashiri Alya Qari Suzan Alhomadi Hisham Alkuraya Mohammed Alsebayel Muddathir H Hamad Laszlo Szonyi Faisal Abaalkhail Sulaiman M Al-Mayouf Hamad Almojalli Khalid S Alqadi Hussien Elsiesy Taghreed M Shuaib Mohammed Zain Seidahmed Ibraheem Abosoudah Hana Akleh Abdulaziz AlGhonaium Turki M Alkharfy Fuad Al Mutairi Wafa Eyaid Abdullah Alshanbary Farrukh R Sheikh Fahad I Alsohaibani Abdullah Alsonbul Saeed Al Tala Soher Balkhy Randa Bassiouni Ahmed S Alenizi Maged H Hussein Saeed Hassan Mohamed Khalil Brahim Tabarki Saad Alshahwan Amira Oshi Yasser Sabr Saad Alsaadoun Mustafa A Salih Sarar Mohamed Habiba Sultana Abdullah Tamim Moayad El-Haj Saif Alshahrani Dalal K Bubshait Majid Alfadhel Tariq Faquih Mohamed El-Kalioby Shazia Subhani Zeeshan Shah Nabil Moghrabi Brian F Meyer Fowzan S Alkuraya

Hum Genet 2017 08 9;136(8):921-939. Epub 2017 Jun 9.

Deparment of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.

In this study, we report the experience of the only reference clinical next-generation sequencing lab in Saudi Arabia with the first 1000 families who span a wide-range of suspected Mendelian phenotypes. A total of 1019 tests were performed in the period of March 2016-December 2016 comprising 972 solo (index only), 14 duo (parents or affected siblings only), and 33 trio (index and parents). Multigene panels accounted for 672 tests, while whole exome sequencing (WES) represented the remaining 347 tests. Pathogenic or likely pathogenic variants that explain the clinical indications were identified in 34% (27% in panels and 43% in exomes), spanning 279 genes and including 165 novel variants. While recessive mutations dominated the landscape of solved cases (71% of mutations, and 97% of which are homozygous), a substantial minority (27%) were solved on the basis of dominant mutations. The highly consanguineous nature of the study population also facilitated homozygosity for many private mutations (only 32.5% of the recessive mutations are founder), as well as the first instances of recessive inheritance of previously assumed strictly dominant disorders (involving ITPR1, VAMP1, MCTP2, and TBP). Surprisingly, however, dual molecular diagnosis was only observed in 1.5% of cases. Finally, we have encountered candidate variants in 75 genes (ABHD6, ACY3, ADGRB2, ADGRG7, AGTPBP1, AHNAK2, AKAP6, ASB3, ATXN1L, C17orf62, CABP1, CCDC186, CCP110, CLSTN2, CNTN3, CNTN5, CTNNA2, CWC22, DMAP1, DMKN, DMXL1, DSCAM, DVL2, ECI1, EP400, EPB41L5, FBXL22, GAP43, GEMIN7, GIT1, GRIK4, GRSF1, GTRP1, HID1, IFNL1, KCNC4, LRRC52, MAP7D3, MCTP2, MED26, MPP7, MRPS35, MTDH, MTMR9, NECAP2, NPAT, NRAP, PAX7, PCNX, PLCH2, PLEKHF1, PTPN12, QKI, RILPL2, RIMKLA, RIMS2, RNF213, ROBO1, SEC16A, SIAH1, SIRT2, SLAIN2, SLC22A20, SMDT1, SRRT, SSTR1, ST20, SYT9, TSPAN6, UBR4, VAMP4, VPS36, WDR59, WDYHV1, and WHSC1) not previously linked to human phenotypes and these are presented to accelerate post-publication matchmaking. Two of these genes were independently mutated in more than one family with similar phenotypes, which substantiates their link to human disease (AKAP6 in intellectual disability and UBR4 in early dementia). If the novel candidate disease genes in this cohort are independently confirmed, the yield of WES will have increased to 83%, which suggests that most "negative" clinical exome tests are unsolved due to interpretation rather than technical limitations.

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Source
http://dx.doi.org/10.1007/s00439-017-1821-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502059PMC
August 2017
8 Citations
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