Substance Use Disorders (SUD)

& Preventive Health Screening

Test Information Sheet

Whole Exome Sequencing (WES), Microarray and

Specialized SUD (Substance Use Disorders) Assay



According to the DSM-5, a “substance use disorder describes a problematic pattern of using alcohol or another substance that results in impairment in daily life or noticeable distress.” The Substance Use Disorders & Preventive Health Screening test is indicated for all individuals who would like to gain insights about their carrier status or predisposition status for substance use disorders, and other health risks recommended for screening by the ACMG. With this knowledge the test subject and his or her healthcare providers and counselors could personalize their health and substance use rehabilitation management plan by implementing lifestyle modifications or treatments to prevent these disorders or improve the test subject’s current health state.


Whole exome sequencing (WES) can be used to analyze most of the genes in an individual at one time to identify the mutation(s) that are causing a genetic disorder or for health screening purposes. This test is most appropriate for generally healthy individuals or those with a family history of certain medical conditions who would like to be screened for the ACMG recommended actionable conditions for prevention purposes. WES targets the protein-coding regions of the genome, which represents approximately 20,000 genes and about 2% of the genome. Individual exons of each gene are initially captured or separated from the rest of the genome and analyzed using massively parallel sequencing. The patient’s sequence is then compared to the reference genome sequence to identify variants that are different and are therefore, potentially causative in the patient’s condition. Ideally, this test is performed by sequencing the patient and both parents (trios) together to identify de novo variants, assign phase to inherited variants for autosomal recessive inheritance or to determine autosomal dominant or X-linked inheritance. However, depending upon the availability of the parents, other family members may also be utilized to maximize the chance of identifying causative variants in the patient.


Microarray and Specialized Substance Use Disorders Assay allows for the genotyping of specific variations or polymorphisms associated with substance use or addiction disorders in the genome of an individual (Table 1). It is different from WES in that specific variants are targeted either within the protein-coding regions or in the non-coding regions of the genome.


Test Method:

WES will be performed on the patient and their family members to target the exonic regions of their genomes. These regions will be sequenced using the Illumina NovaSeq 6000 with 100-150 bp paired-end reads. The DNA sequence will then be mapped to, and analyzed in comparison with, the published human genome build (UCSC hg19 reference sequence). The targeted coding exons and splice junctions of the known protein-coding RefSeq genes will be assessed for the average depth of coverage (minimum average coverage of 80X for WES and 15X-30X for WGS) and data quality threshold values. Sequence changes in the patient will be compared to the other provided family members. All reportable sequence variants will be confirmed by Sanger sequence analysis using a separate DNA preparation. Average quality thresholds may range from >90-95% of the targeted region, indicating a small portion of the target region may not be covered with sufficient depth or quality to confidently call variant positions. In addition to Next Generation Sequencing (NGS) for capturing the whole exome, microarray method using Illumina iScan technology, as well as a custom designed assay will be used to capture regions of the genome that are within and outside of the protein coding genes (i.e. intergenic). SNPs (Single Nucleotide Polymorphisms) or variants from the microarray and custom assay data will also be used in the analysis to generate parts of this report. The sequencing, genotyping, alignment and variant calling of the data will be performed at the Gene by Gene, Ltd. laboratory located in 1445 North Loop West, Suite 760 Houston, TX 77008. Analysis, interpretation and report will be performed by TOVANA HEALTH located at 945 McKinney St. Suite# 11977 Houston, TX 77002.



Absence of a causative variant(s) related to the reported phenotype by the WES and microarray methods does not exclude a genetic basis of the individual’s condition. Some types of genetic abnormalities, such as copy number changes, trinucleotide repeat expansions, small insertion/deletions and X-linked recessive mutations which manifest in females due to skewed X-inactivation may not be detectable with the technologies utilized for this testing. This test does not analyze mitochondrial DNA sequence or epigenetic changes of the genome. It is possible that the genomic region where a disease-causing mutation exists in the proband was not captured or accurately mapped to the reference sequence using the current technologies and therefore was not detected. Additionally, it is possible that a particular genetic abnormality may not be recognized as the underlying cause of the genetic disorder due to incomplete scientific knowledge about the function of all genes in the human genome and the impact of variations in those genes. Variants in genes associated with substance use disorders are included in this report (Table 1). In addition, based on the consent process, this individual may have opted to receive clinically relevant incidental findings that are actionable or preventive health conditions, not related to the substance use disorder phenotype in this individual, and may have also been included in this report (Table 2). This report has been evaluated and accredited by the College of American Pathologists (CAP) for the clinical whole exome and clinical microarray sections of the report, but not the non-clinical sections (i.e. Substance Use Disorder Traits section).


Table 1 – List of Substance Use Disorder (SUD) categories and traits genetically screened


SUD Category SUD Trait
Smoking Behavior Nicotine Dependence
Smoking Behavior Smoking Cessation (former smoking status)
Smoking Behavior Cigarettes Per Day (CPD)
Smoking Behavior Nicotine metabolite ratio (NMR)
Alcohol Use Disorder Alcohol Consumption (drinks/week)
Alcohol Use Disorder MaxDrinks (Maximum drinks in a 24-hour period)
Alcohol Use Disorder Alcohol Dependence (AD)
Alcohol Use Disorder Flushing response to alcohol
Alcohol Use Disorder Drinker Behavior (likely to report consuming alcohol)
Cannabis Use Disorder Cannabis Dependence (CAD)
Stimulant Use Disorder Cocaine Dependence (CD)
Opioid Use Disorder Opioid Dependence/Addiction
Polysubstance Use Disorder Polysubstance Dependence/Addiction
Polysubstance Use Disorder Polysubstance Drug Abuse



Table 2 – List of 59 conditions recommended for testing by the American College of Medical Genetics and Genomics (ACMG)


Disease name and MIM Number Gene and MIM Number
Adenomatous polyposis coli (MIM 175100) APC (MIM 611731)
Aortic aneurysm, familial thoracic 4 (MIM 132900) MYH11 (MIM 160745)
Aortic aneurysm, familial thoracic 6 (MIM 611788) ACTA2 (MIM 102620)
Arrhythmogenic right ventricular cardiomyopathy, type 5 (MIM 604400) TMEM43 (MIM 612048)
Arrhythmogenic right ventricular cardiomyopathy, type 8 (MIM 607450) DSP (MIM 125647)
Arrhythmogenic right ventricular cardiomyopathy, type 9 (MIM 609040) PKP2 (MIM 602861)
Arrhythmogenic right ventricular cardiomyopathy, type 10 (MIM 610193) DSG2 (MIM 125671)
Arrhythmogenic right ventricular cardiomyopathy, type 11 (MIM 610476) DSC2 (MIM 125645)
Breast-ovarian cancer, familial 1 (MIM 604370) BRCA1 (MIM 113705)
Breast-ovarian cancer, familial 2 (MIM 612555) BRCA2 (MIM 600185)
Brugada syndrome 1 (MIM 601144) SCN5A (MIM 600163)
Catecholaminergic polymorphic ventricular tachycardia (MIM 604772) RYR2 (MIM 180902)
Dilated cardiomyopathy 1A (MIM 115200) LMNA (MIM 150330)
MYBPC3 (MIM 600958)
Ehlers-Danlos syndrome, type 4 (MIM 130050) COL3A1 (MIM 120180)
Fabry’s disease (MIM 301500) GLA (MIM 300644)
Familial hypercholesterolemia (MIM 143890) APOB (MIM 107730)
LDLR (MIM 606945)
Familial hypertrophic cardiomyopathy 1 (MIM 192600) MYH7 (MIM 160760)
Familial hypertrophic cardiomyopathy 3 (MIM 115196) TPM1 (MIM 191010)
Familial hypertrophic cardiomyopathy 4 (MIM 115197) MYBPC3 (MIM 600958)
Familial hypertrophic cardiomyopathy 6 (MIM 600858) PRKAG2 (MIM 602743)
Familial hypertrophic cardiomyopathy 7 (MIM 613690) TNNI3 (MIM 191044)
Familial hypertrophic cardiomyopathy 8 (MIM 608751) MYL3 (MIM 160790)
Familial hypertrophic cardiomyopathy 10 (MIM 608758) MYL2 (MIM 160781)
Familial hypertrophic cardiomyopathy 11 (MIM 612098) ACTC1 (MIM 102540)
Familial medullary thyroid carcinoma (MIM 155240) RET (MIM 164761)
Hypercholesterolemia, autosomal dominant, 3 (MIM 603776) PCSK9 (MIM 607786)
Juvenile polyposis (MIM 174900) BMPR1A (MIM 601299)
SMAD4 (MIM 600993)
Left ventricular noncompaction 6 (MIM 601494) TNNT2 (MIM 191045)
Li-Fraumeni syndrome 1 (MIM 151623) TP53 (MIM 191170)
Loeys-Dietz syndrome type 1A (MIM 609192) TGFBR1 (MIM 190181)
Loeys-Dietz syndrome type 1B (MIM 610168) TGFBR2 (MIM 190182)
Loeys-Dietz syndrome type 2A (MIM 608967) TGFBR1 (MIM 190181)
Loeys-Dietz syndrome type 2B (MIM 610380) TGFBR2 (MIM 190182)
Loeys-Dietz syndrome type 3 (MIM 613795) SMAD3 (MIM 603109)
Long QT syndrome 1 (MIM 192500) KCNQ1 (MIM 607542)
Long QT syndrome 2 (MIM 613688) KCNH2 (MIM 152427)
Long QT syndrome 3 (MIM 603830) SCN5A (MIM 600163)
Lynch syndrome (MIM 120435) MLH1 (MIM 120436)
MSH2 (MIM 609309)
MSH6 (MIM 600678)
PMS2 (MIM 600259)
Malignant hyperthermia (MIM 145600) RYR1 (MIM 180901)
CACNA1S (MIM 114208)
Marfan syndrome (MIM 154700) FBN1 (MIM 134797)
TGFBR1 (MIM 190181)
Multiple endocrine neoplasia, type 1 (MIM 131100) MEN1 (MIM 613733)
Multiple endocrine neoplasia, type 2a (MIM 171400) RET (MIM 164761)
Multiple endocrine neoplasia, type 2b (MIM 162300) RET (MIM 164761)
MYH-associated polyposis (MIM 608456) MUTYH (MIM 604933)
Neurofibromatosis, type 2 (MIM 101000) NF2 (MIM 607379)
Ornithine transcarbamylase deficiency (MIM 311250) OTC (MIM 300461)
Paragangliomas 1 (MIM 168000) SDHD (MIM 602690)
Paragangliomas 2 (MIM 601650) SDHAF2 (MIM 613019)
Paragangliomas 3 (MIM 605373) SDHC (MIM 602413)
Paragangliomas 4 (MIM 115310) SDHB (MIM 185470)
Peutz-Jeghers syndrome (MIM 175200) STK11 (MIM 602216)
Pilomatrixoma (MIM 132600) MUTYH (MIM 604933)
PTEN hamartoma tumor syndrome (MIM 153480) PTEN (MIM 601728)
Retinoblastoma (MIM 180200) RB1 (MIM 614041)
Tuberous sclerosis 1 (MIM 191100) TSC1 (MIM 605284)
Tuberous sclerosis 2 (MIM 613254) TSC2 (MIM 191092)
Von Hippel-Lindau syndrome (MIM 193300) VHL (MIM 608537)
Wilms tumor (MIM 194070) WT1 (MIM 607102)
Wilson disease (MIM 277900) ATP7B (MIM 606882)





CATALOG NUMBER: 1100116, 1100016

Extracted DNA: 20ul of 50ng/ul, OD260/OD280 ~ 1.8, include details of extraction method with samples


Blood: 3-5cc drawn in EDTA (purple-top) tube