Method for detection of traumatic brain injury
The present disclosure describes significant methylation changes in multiple genes and multiple metabolites in body fluid in response to TBI. Gene pathways affected included several known to be involved in neurological and brain function. A large number of good to excellent biomarkers for the detection of TBI was identified. The combination of epigenomic, clinical and metabolomic markers in different combinations overall were highly accurate for the detection of pediatric concussion using Artificial Intelligence-based techniques.
1. A method for diagnosing and treating traumatic brain injury (TBI), wherein the method comprises
assaying a biological sample from a patient in need of TBI diagnosis comprising nucleic acids to determine a frequency or percentage methylation of cytosine at two or more loci throughout genome;
comparing the cytosine methylation level of the sample to cytosine methylation level of a control sample thereby diagnosing TBI in the patient, wherein the control sample is a corresponding biological sample from a healthy subject wherein difference in cytosine methylation level between the biological sample and control sample at two or more loci is greater than 2%, and wherein the two or more loci comprise two or more of the following loci: cg06393885, cg20569893, cg00611535, and/or cg16882751; and
treating the patient, wherein treating the patient comprises cognitive and physical rest and aerobic treatment, post traumatic headache management and treatment, cognitive impairment treatment, vestibulo-oculomotor dysfunction treatment, or sleep deprivation treatment.
2. The method of claim 1 , wherein the method further comprises extracting nucleic acids from the biological sample.
3. The method of claim 1 , wherein the TBI comprises chronic traumatic encephalopathy (CTE), recurrent TBI, or mild TBI (mTBI).
4. The method of claim 1 , wherein the method further comprises calculating the patient's risk of TBI based on the cytosine methylation level at different sites throughout the genome.
5. The method of claim 1 , wherein the biological sample comprises body fluid or a tissue obtained from the patient.
6. The method of claim 1 , wherein the biological sample comprises blood, plasma, serum, cerebral spinal fluid, buccal swab, saliva, sputum, urine, tear, sweat, or hair.
7. The method of claim 1 , wherein the biological sample is from a patient of greater than 19 years old or wherein the biological sample is from a pediatric patient.
8. The method of claim 1 , wherein the nucleic acids comprise cellular nucleic acids or wherein the nucleic acids comprise cell free nucleic acids.
9. The method of claim 1 , wherein each of the loci comprises an AUC of 0.75 or greater, 0.80 or greater, 0.85 or greater, 0.90 or greater, or 0.95 or greater.
10. The method of claim 1 , wherein the assay is a bisulfite-based methylation assay or a whole genome methylation assay.
11. The method of claim 1 , wherein measurement of the frequency or percentage methylation of cytosine nucleotides is obtained using single gene or whole genome sequencing techniques.
12. A method of claim 1 , wherein the method further comprises assaying proteins encoded by the nucleic acids comprising the differentially methylated CpG loci, or assaying mRNA comprising the differentially methylated CpG loci.
13. The method of claim 1 , wherein the method further comprises assaying for one or more metabolomic markers.
14. The method of claim 1 , wherein the method further comprises using artificial intelligence techniques.
15. The method of claim 14 , wherein using artificial intelligence techniques comprises using one or more of the following machine learning algorithms: Random Forest (RF), Support Vector Machine (SVM), Linear Discriminant Analysis (LDA), Prediction of Analysis for Microarrays (PAM), Generalized Linear Model (GLM), or deep learning (DL).
16. The method of claim 1 , wherein the two or more loci comprise cg06393885, cg20569893, cg00611535, and cg16882751.
17. The method of claim 1 , wherein the loci further comprise one or more of the following loci: cg24402518, cg20601481, cg05138188, cg27384352, cg24684739, cg13528854, cg24104241, cg24684739, cg18419977, cg07077221, cg03957481, cg19470964, cg06233996, cg24742298, cg15531403, and cg16117781.
18. The method of claim 16 , wherein the loci further comprise one or more of the following loci: cg24402518, cg20601481, cg05138188, cg27384352, cg24684739, cg13528854, cg24104241, cg24684739, cg18419977, cg07077221, cg03957481, cg19470964, cg06233996, cg24742298, cg15531403, and cg16117781.