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Mitochondrial/Metabolic Oligonucleotide Array CGH Analysis

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® Mitochondrial/Metabolic oligonucleotide array CGH analysis MitoMet® oligo aCGH disorder list ® One Baylor Plaza, Nab 2015, Houston, Texas 77030 One Baylor Plaza, Nab 2015, Houston, Texas713-798-6555 77030 • 713-798-6555 • 1-800-411-gene • 1-800-411-gene (4363) (4363) • www.bcmgeneticlabs.org b a y l o r c ollege of Medicine www.bcmgeneticlabs.org Medical Genetic Laboratories Genetic Medical Medicine of College Baylor he MitoMet® array contains Indications for Testing: muscle and liver are recommended. 1. MitoMet® aCGH analysis is Analysis on MitoMet® array will 60,000 oligonucleotide recommended for autosomal detect heteroplasmic mtDNA probes targeted to both mitochondrial recessive cases with one identified deletions. The analysis will also point mutation or apparent reveal approximate breakpoints and nuclear genes involved in homozygote. and copy number. mitochondrial and metabolic related 2. For autosomal dominant cases, Limitation of Testing: diseases. Approximately 3200 probes MitoMet® aCGH analysis of samples This analysis will not detect point negative on full gene sequence mutations or small deletion/duplication cover the entire 16.6 kb mitochondrial will detect heterozygous intragenic mutations. For mtDNA, the deletion of genome in the forward direction. In deletion or duplication. less than 200 bp and for nuclear genes deletion less than 300 kb may not be addition, the current array includes an 3. MitoMet® aCGH analysis is detected. Heteroplasmy of less than average exon coverage of about 6/exon recommended for cases where 15% may not be detected. PCR fails to amplify regions for oligo probes targeted to approximately sequence analysis. Testing Methodology: The data are analyzed using quantitative 4. MitoMet® aCGH analysis is imaging methods and analytical recommended for cases where software to assist in identifying each intragenic or multigenic compound targeted-DNA sequence as loss of heterozygous deletions or copy number (deletion in nuclear gene duplications are suspected. and depletion in mtDNA), gain of copy number (duplication in nuclear gene or 5. Quick screening for mitochondrial over-amplification in mtDNA) or normal DNA deletions and depletions. copy number. The relevant tissues such as 350 genes that are involved in mtDNA Specimen Requirements: Blood: EDTA (purple-top) tubes: Adult: 14 cc; Child/Infant: 6 cc biogenesis, maintenance of mitochondrial deoxynucleotide pools, mitochondrial Turnaround Time: transcription and translation factors, Turnaround times are available on our web site: www.bcmgeneticlabs.org respiratory chain complex assembly E-mail: [email protected] • Phone: (713) 798-5849 • Fax: (713) 798-4187 Baylor College of Medicine Medical Genetic Laboratories and complex subunits, urea cycle Shipping Information disorders, fatty acid oxidation, amino Forms: acid metabolism, creatine pathway, Mitochondrial Requisition - Mitochondrial Diagnostic Checklist is included progressive familial intrahepatic Test Code: cholestasis, newborn screening diseases, Index: 3500 plus many more. This array detects Known Familial Mutation: 3501 Prenatal: 3502 intragenic nuclear gene deletions/ duplications larger than 1 kb and mtDNA deletions larger than 200 bp. MitoMet® oligo aCGH V2.8 1 Disorder List Baylor College of Medicine Medical Genetic Laboratories Disorder Gene Disorder GENE COORDINATES OMIM# OMIM* AARS2 *612035 Chr. 6: 44,374,441-44,389,041 Progressive Familial Intrahepatic Cholestasis 2 (PFIC2) #601847 ABCB11 *603201 Chr. 2: 169,487,694-169,596,079 Progressive Familial Intrahepatic Cholestasis 3 (PFIC3) #602347 ABCB4 *171060 Chr. 7: 86,869,302-86,942,991 X-Linked Sideroblastic Anemia and Spinocerebellar Ataxia #301310 ABCB7 *300135 Chr. X: 74,189,834-74,292,857 Long Chain Acyl-CoA Dehydrogenase Dificiency (LCAD) #201460 ACADL *609576 Chr. 2: 210,760,963-210,798,405 Medium Chain Acyl-CoA Dehydrogenase Deficiency (MCAD) #201450 ACADM *607008 Chr. 1: 75,962,982-76,001,763 Short Chain Acyl-CoA Dehydrogenase Deficiency (SCAD) #201470 ACADS *606885 Chr. 12: 119,648,025-119,662,193 Short/Branched Chain Acyl-CoA Dehydrogenase Deficiency #610006 ACADSB *600301 Chr. 10: 124,758,419-124,807,796 (SBCAD) Very Long Chain Acyl-CoA Dehydrogenase Deficiency (VLCAD) #201475 ACADVL *609575 Chr. 17: 7,063,877-7,069,308 Mitochondrial Adenylate Kinase-2 AK2 *103020 Chr. 1: 33,246,173-33,275,079 Hereditary Fructose Intolerance #229600 ALDOB *612724 Chr. 9: 103,223,480-103,237,926 Ataxia with Oculomotor Apraxia 1 (AOA1) #208920 APTX *606350 Chr. 9: 32,962,609-32,991,626 Arginase Deficiency #207800 ARG1 *608313 Chr. 6: 131,936,058-131,947,161 Argininosuccinic Aciduria #207900 ASL *608310 Chr. 7: 65,178,249-65,195,375 Citrullinemia Type 1 #215700 ASS1 *603470 Chr. 9: 132,310,170-132,366,482 ATP12A *182360 Chr. 13: 24,152,695-24,183,918 Progressive Familial Intrahepatic Cholestasis 1 (PFIC1) #211600 ATP8B1 *602397 Chr. 18: 53,464,656-53,550,037 Mitochondrial Respiratory Chain Deficiency, Complex V #604273 ATPAF2 *608918 Chr. 17: 17,862,059-17,883,205 3-Methylglutaconic Aciduria (MGA) Type I #250950 AUH *600529 Chr. 9: 93,015,926-93,163,996 Maple Syrup Urine Disease, Type 1a #248600 BCKDHA *608348 Chr. 19: 46,595,544-46,622,749 Gracile Syndrome #603358 BCS1L *603647 Chr. 2: 219,232,676-219,236,410 Leigh Syndrome (nuclear genes) #256000 BCS1L *603647 Chr. 2: 219,232,676-219,236,410 Mitochondrial Respiratory Chain Complex III Deficiency, #124000 BCS1L *603647 Chr. 2: 219,232,676-219,236,410 BCS1L Related Biotinidase Deficiency #253260 BTD *609019 Chr. 3: 15,618,259-15,662,328 Mitochondrial Complex I Deficiency #252010 C6orf66 *611776 Chr. 6: 97,445,612-97,452,476 C11orf79 Hereditary Paragangliomas 2 #601650 *613019 Chr. 11: 60,954,173-60,970,801 (SDH5) C12orf65 Chr. 12: 122,283,416-122,308,459 C14orf156 *610211 Chr. 14: 77,244,188-77,253,690 C18orf22 Chr. 18: 75,895,346-75,907,373 CARS2 *612800 Chr. 13: 110,091,760-110,156,464 Homocystinuria, Cystathionine Beta-Synthase Deficiency CBS *236200 Chr. 21: 43,346,370-43,369,541 CCDC44 Leigh Syndrome (nuclear genes) #256000 *612958 Chr. 17: 59,031,973-59,039,456 (TACO1) Cardiomyopathy-associated protein 5 CMYA5 *612193 Chr. 5: 79,021,415-79,131,804 Coenzyme Q10 Deficiency #607426 COQ2 *609825 Chr. 4: 84,404,003-84,425,091 Coenzyme Q10 Deficiency (CABC1) #607426 COQ8 *606980 Chr. 1: 225,194,561-225,241,869 Spinocerebellar Ataxia (CABC1) #612016 COQ8 *606980 Chr. 1: 225,194,561-225,241,869 Coenzyme Q10 Deficiency #607426 COQ9 *612837 Chr. 16: 56,038,903-56,052,679 COX4I1 *123864 Chr. 16: 84,390,697-84,398,109 Exocrine Pancreatic Insufficiency #612714 COX4I2 *607976 Chr. 20: 29,689,352-29,696,461 One Baylor Plaza, Nab 2015, Houston, Texas 77030 • 713-798-6555 • 1-800-411-gene (4363) • www.bcmgeneticlabs.org MitoMet® oligo aCGH V2.8 2 Disorder List Baylor College of Medicine Medical Genetic Laboratories Disorder Gene Disorder GENE COORDINATES OMIM# OMIM* COX5A *603773 Chr. 15: 72,999,672-73,017,438 COX5B *123866 Chr. 2: 97,628,953-97,631,086 COX6A1 *602072 Chr. 12: 119,360,287-119,362,915 COX6A2 *602009 Chr. 16: 31,346,556-31,347,222 Mitochondrial Respiratory Chain Complex IV #220110 COX6B1 *124089 Chr. 19: 40,830,995-40,841,523 Deficiency (nuclear genes) COX6B2 Chr. 19: 60,552,888-60,557,994 COX6C *124090 Chr. 8: 100,959,548-100,975,071 COX7A1 *123995 Chr. 19: 41,333,664-41,335,611 COX7A2 *123996 Chr. 6: 76,004,223-76,010,245 COX7A2L *605771 Chr. 2: 42,431,146-42,441,860 COX7B *603792 Chr. X: 77,041,627-77,047,537 COX7B2 *609811 Chr. 4: 46,431,606-46,606,009 COX7C *603774 Chr. 5: 85,949,540-85,952,337 COX8A *123870 Chr. 11: 63,498,655-63,500,590 (COX8) COX8C Chr. 14: 92,883,290-92,884,453 Leigh Syndrome (nuclear genes) #256000 COX10 *602125 Chr. 17: 13,913,444-14,052,712 Mitochondrial Respiratory Chain Complex IV Deficiency (nuclear #220110 COX10 *602125 Chr. 17: 13,913,444-14,052,712 genes) COX11 *603648 Chr. 17: 50,384,266-50,401,053 Leigh Syndrome (nuclear genes) #256000 COX15 *603646 Chr. 10: 101,461,596-101,481,890 Mitochondrial Respiratory Chain Complex IV Deficiency #220110 COX15 *603646 Chr. 10: 101,461,596-101,481,890 (nuclear genes) COX17 *604813 Chr. 3: 120,871,062-120,878,933 COX18 *610428 Chr. 4: 74,139,280-74,154,336 COX19 *610429 Chr. 7: 971,012-981,761 Carbamoyl-phosphate Synthetase I Deficiency #237300 CPS1 *608307 Chr. 2: 211,129,583-211,252,074 Carnitine Palmitoyltransferase IA Deficiency #255120 CPT1A *600528 Chr. 11: 68,278,666-68,365,850 CPT1B *601987 Chr. 22: 49,354,156-49,363,744 Carnitine Palmitoyltransferase II Deficiency, Late Onset #255110 CPT2 *600650 Chr. 1: 53,434,689-53,452,455 Carnitine Palmitoyltransferase II Deficiency, Infantile #600649 CPT2 *600650 Chr. 1: 53,434,689-53,452,455 Carnitine Palmitoyltransferase II Deficiency, Lethal Neonatal #608836 CPT2 *600650 Chr. 1: 53,434,689-53,452,455 Thrombocytopenia; autosomal dominant, 4 #612004 CYCS *123970 Chr. 7: 25,124,802-25,131,480 DAP3 *602074 Chr. 1: 153,925,506-153,974,941 (MRPS29) Leukoencephalopathy with Brainstem and Spinal Cord Involvement #611105 DARS2 *610956 Chr. 1: 172,060,581-172,094,305 and Lactate Elevation Maple Syrup Urine Disease, Type II #248600 DBT *248610 Chr. 1: 100,425,072-100,487,997 Mitochondrial DNA Depletion Syndrome, Hepatocerebral Form #251880 DGUOK *601465 Chr. 2: 74,007,461-74,039,596 Maple Syrup Urine Disease, Type III #248600 DLD *238331 Chr. 7: 107,318,822-107,348,879 Leigh Syndrome (nuclear genes) #256000 DLD *238331 Chr. 7: 107,318,822-107,348,879 DNA2 *601810 Chr. 10: 69,843,827-69,901,885 One Baylor Plaza, Nab 2015, Houston, Texas 77030 • 713-798-6555 • 1-800-411-gene (4363) • www.bcmgeneticlabs.org MitoMet® oligo aCGH V2.8 3 Disorder List Baylor College of Medicine Medical Genetic Laboratories Disorder Gene Disorder GENE COORDINATES OMIM# OMIM* 3-Methylglutaconic Aciduria (MGA) Type V #610198 DNAJC19 *608977 Chr.
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    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
  • Abstracts from the 50Th European Society of Human Genetics Conference: Electronic Posters

    Abstracts from the 50Th European Society of Human Genetics Conference: Electronic Posters

    European Journal of Human Genetics (2019) 26:820–1023 https://doi.org/10.1038/s41431-018-0248-6 ABSTRACT Abstracts from the 50th European Society of Human Genetics Conference: Electronic Posters Copenhagen, Denmark, May 27–30, 2017 Published online: 1 October 2018 © European Society of Human Genetics 2018 The ESHG 2017 marks the 50th Anniversary of the first ESHG Conference which took place in Copenhagen in 1967. Additional information about the event may be found on the conference website: https://2017.eshg.org/ Sponsorship: Publication of this supplement is sponsored by the European Society of Human Genetics. All authors were asked to address any potential bias in their abstract and to declare any competing financial interests. These disclosures are listed at the end of each abstract. Contributions of up to EUR 10 000 (ten thousand euros, or equivalent value in kind) per year per company are considered "modest". Contributions above EUR 10 000 per year are considered "significant". 1234567890();,: 1234567890();,: E-P01 Reproductive Genetics/Prenatal and fetal echocardiography. The molecular karyotyping Genetics revealed a gain in 8p11.22-p23.1 region with a size of 27.2 Mb containing 122 OMIM gene and a loss in 8p23.1- E-P01.02 p23.3 region with a size of 6.8 Mb containing 15 OMIM Prenatal diagnosis in a case of 8p inverted gene. The findings were correlated with 8p inverted dupli- duplication deletion syndrome cation deletion syndrome. Conclusion: Our study empha- sizes the importance of using additional molecular O¨. Kırbıyık, K. M. Erdog˘an, O¨.O¨zer Kaya, B. O¨zyılmaz, cytogenetic methods in clinical follow-up of complex Y.
  • Blueprint Genetics BCS1L Single Gene Test

    Blueprint Genetics BCS1L Single Gene Test

    BCS1L single gene test Test code: S00213 Phenotype information Bjornstad syndrome GRACILE syndrome Leigh syndrome Mitochondrial complex III deficiency, nuclear type 1 Alternative gene names BCS, BJS, Hs.6719, h-BCS Panels that include the BCS1L gene Syndromic Hearing Loss Panel Comprehensive Hearing Loss and Deafness Panel Resonate Program Panel 3-M Syndrome / Primordial Dwarfism Panel Ectodermal Dysplasia Panel Comprehensive Growth Disorders / Skeletal Dysplasias and Disorders Panel Comprehensive Metabolism Panel Organic Acidemia/Aciduria & Cobalamin Deficiency Panel Comprehensive Short Stature Syndrome Panel Non-coding disease causing variants covered by the test Gene Genomic location HG19 HGVS RefSeq RS-number BCS1L Chr2:219524871 c.-147A>G NM_004328.4 BCS1L Chr2:219525123 c.-50+155T>A NM_004328.4 rs386833855 Test Strengths The strengths of this test include: CAP accredited laboratory CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance Careful construction of clinically effective and scientifically justified gene panels Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level Our publicly available analytic validation demonstrating complete details of test performance ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see ‘Non-coding disease causing variants
  • Molecular Diagnostic Requisition

    Molecular Diagnostic Requisition

    BAYLOR MIRACA GENETICS LABORATORIES SHIP TO: Baylor Miraca Genetics Laboratories 2450 Holcombe, Grand Blvd. -Receiving Dock PHONE: 800-411-GENE | FAX: 713-798-2787 | www.bmgl.com Houston, TX 77021-2024 Phone: 713-798-6555 MOLECULAR DIAGNOSTIC REQUISITION PATIENT INFORMATION SAMPLE INFORMATION NAME: DATE OF COLLECTION: / / LAST NAME FIRST NAME MI MM DD YY HOSPITAL#: ACCESSION#: DATE OF BIRTH: / / GENDER (Please select one): FEMALE MALE MM DD YY SAMPLE TYPE (Please select one): ETHNIC BACKGROUND (Select all that apply): UNKNOWN BLOOD AFRICAN AMERICAN CORD BLOOD ASIAN SKELETAL MUSCLE ASHKENAZIC JEWISH MUSCLE EUROPEAN CAUCASIAN -OR- DNA (Specify Source): HISPANIC NATIVE AMERICAN INDIAN PLACE PATIENT STICKER HERE OTHER JEWISH OTHER (Specify): OTHER (Please specify): REPORTING INFORMATION ADDITIONAL PROFESSIONAL REPORT RECIPIENTS PHYSICIAN: NAME: INSTITUTION: PHONE: FAX: PHONE: FAX: NAME: EMAIL (INTERNATIONAL CLIENT REQUIREMENT): PHONE: FAX: INDICATION FOR STUDY SYMPTOMATIC (Summarize below.): *FAMILIAL MUTATION/VARIANT ANALYSIS: COMPLETE ALL FIELDS BELOW AND ATTACH THE PROBAND'S REPORT. GENE NAME: ASYMPTOMATIC/POSITIVE FAMILY HISTORY: (ATTACH FAMILY HISTORY) MUTATION/UNCLASSIFIED VARIANT: RELATIONSHIP TO PROBAND: THIS INDIVIDUAL IS CURRENTLY: SYMPTOMATIC ASYMPTOMATIC *If family mutation is known, complete the FAMILIAL MUTATION/ VARIANT ANALYSIS section. NAME OF PROBAND: ASYMPTOMATIC/POPULATION SCREENING RELATIONSHIP TO PROBAND: OTHER (Specify clinical findings below): BMGL LAB#: A COPY OF ORIGINAL RESULTS ATTACHED IF PROBAND TESTING WAS PERFORMED AT ANOTHER LAB, CALL TO DISCUSS PRIOR TO SENDING SAMPLE. A POSITIVE CONTROL MAY BE REQUIRED IN SOME CASES. REQUIRED: NEW YORK STATE PHYSICIAN SIGNATURE OF CONSENT I certify that the patient specified above and/or their legal guardian has been informed of the benefits, risks, and limitations of the laboratory test(s) requested.