GENE UNIVERSE

Helping people understand their personal genomic data

Why you should get your DNA analyzed:

Disease predisposition - to understand which diseases you may have a predisposition for and take action to prevent them from developing
Carrier status - to determine if you are a carrier for a genetic disease to avoid passing it on to your children
Participate in scientific research - you can voluntarily provide access of your data to researchers to help understand the cause of genetic diseases and traits
Precursor to genetic engineering - it will soon be possible to modify your DNA to prevent or treat genetic diseases
Self understanding - to get a better understanding of your personal biology

Where can I get my genome analyzed direct-to-consumer (without going through a doctor) and what is the cost?

Nebula Genomics - whole genome sequencing, about $500 for data and analysis, their reporting includes polygenic risk scores, but no carrier status or X-linked status, you can also download your raw sequence data
23andMe - well established company, cost = $230 for basic health and ancestry; they have good analysis and reporting, however they look at only part of genome (genotyping) - not the whole genome
Dante Labs - whole genome sequencing, $400 for sequencing and basic analysis,extra cost for additional analyses, it took about 3 months to get my report back after sending in my sample
Sequencing.com - whole genome sequencing, cost about $400 for the basic sequencing and analysis, more money for additional reports or faster turn around time - still looking into this company

How can I analyze my genome data myself?

Many companies provide the capability to download your raw genomic data and analyze it yourself - for example, 23andMe and Nebula allow this
Once, you have downloaded your 23andMe data, you can manually look up the data on a free database such as dbSNP
Alternatively, you can upload your 23andMe raw data to another third party web site that provdes free or inexpensive analysis - such as Promethease, Selfdecode, Genomelink
You can manually browse whole genome sequence (WGS) data for free in IGV (Integrative Genomics Viewer)
You can upload your WGS data to Sequencing.com for third party analysis
There are many independent DNA analysis tools you can find on the web by doing a Google search

The human genome summary:

23 chromosome pairs
3.2 billion base pairs
22,000 genes.
All humans are about 99.9% identical in terms of their DNA. The remaining .1% determines the differences between individuals.
types of variations include: single nucleotide variations, insertions, deletions, multiple copies of short sequences, inversions, translocations, chromosome anomalies
most genetics traits and common diseases are caused by variations in multiple genes ( polygenic)
some relatively rare diseases are caused by mutations in single genes
only 2 to 3% of the DNA codes for proteins - the rest of the DNA has regulatory or unknown functionality
most of the common/ complex disease or traits are cause by variations in the regulatory regions of the DNA

Some diseases caused by variants in a single gene (monogenic)

Disease	Gene	Inheritance pattern	number in USA	number in world
Achrondoplasia dwarfism	FGFR3	autosomal dominant - usually new mutation	15,000	250,000
Beta Thalassemia	HBB	autosomal recessive	1,200	100,000
Cystic Fibrosis	CFTR	autosomal recessive	40,000	160,000
Duchenne muscular dystrophy	DMD	X linked	less than 50,000	20,000 diagnosed each year
Familial adenomatous polyposis	APC	autosomal dominant	50,000
Fragile X syndrome	FMR1	X linked	38,000 to 87,000	777,000 to 1,400,000
Hemochromatosis Type 1	HFE	autosomal recessive	1 in 300
Huntington's disease	HTT (excessive CAG repeats)	autosomal dominant	30,000	???
Marfan syndrome	FBN1	autosomal dominant	1 in 5,000	1 in 5,000
Neurofibromatosis Type 1	NF1	automosal dominant	100,000	1 in 3,000
Progeria (premature aging)	LMNA	autosomal dominant - usually new mutation	131	400
Sickle Cell Anemia	HBB	autosomal recessive	100,000	7 million
Spinal Muscular Atrophy	SMN1 and/or SMN2	autosomal recessive	25,000	???
Tay Sachs Disease	HEXA	autosomal recessive	1 in 320,000 newborns

Some diseases caused by variants in more than one gene (polygenic)

Disease	Associated Genes	number in world
Alzheimers - early onset	APP, PSEN1, PSEN2
Alzheimers - late onset	APOE	55 million
Acne - severe	NCSTN, OVOL1, FST, TGFB2, SELL, DDB2	9.4 %
Autism	ADNP, CHD2, CTNND2, DYRK1A, GRIN2B, SYNGAP1	75 million
Charcot-Marie-Tooth disease	PMP22, MPZ, MFN2, GJB1
Diabetes type 1	HLA-DQA1, HLA-DQB1, and HLA-DRB1 genes and some unknown environmental factor - perhaps viral infection	8.4 million
Familial Hyperlipidemia ( high cholesterol )	LDLR, APOB, or PCSK9	1 in 300
Lynch syndrome	MLH1, MSH2, MSH6, PMS2, or EPCAM	1 million US
Multiple Sclerosis	one mechanism is HLA-DR15 gene variant plus Epstein-Barr virus infection	2.8 million
Osteoporosis/low bone density	BMP2, DAAM2, LRP5, VDR, ESR1	200 million
Schizophrenia	GRIN2A, SP4, GRIA3, DISC1	24 million

Traits determined by variants in multiple genes (polygenic)

Trait	Associated Genes
athletic performance/fast twitch muscle fiber	ACTN3, ACE
eye color	OCA2, HERC2, SLC45A2
hair color	MC1R, SLC45A2
hair curliness	TCHH
height	multiple genes, not well understood yet
intelligence	multiple genes, not well understood yet
longevity	APOE, FOXO3, CETP in addition to lifestyle and environment
male pattern baldness	AR, EDA2R, OPHN1, ZC4H2
muscle strength	ACTG1, PEX14, TGFA, SYT1
skin color	MC1R, MFSD12, OCA2, HERC2, SLC45A2

What are some applications of personal genomics?

Screening for carrier status - many people are carriers for recessive genetic diseases and they don't even know it. For example, Cystic Fibrosis, Sickle Cell Disease and Spinal Muscular Atrophy. If you know your genomic data, you can avoid accidentally passing genetic diseases on to your children.
Pharmacogenetics - not everyone responds the same way to medications. Some people may over-respond to a drug, but others my not respond at all. The different responses are frequently due to genetic variation. If you know your genomic information, you and your doctor can better predict how you will respond to certain drugs.
Cancer diagnosis - most cancers are thought to be caused by DNA mutations in somatic cells. Sequencing of DNA from cancer cells will enable a better identification of the mutations causing the cancer, and therefore a more precise treatment.
Diagnosis of rare diseases - occasionally there is a patient who has a disease or condition which cannot be diagnosed with the normal tests. Sometimes a whole genome sequencing will identify a rare mutation causing the disease, which may lead to treatment
Gene Therapy - with the genetic engineering technology such as CRISPR it is possible to modify a person's DNA. Although this technology is still in the early stages, it will undoubtably be commonplace in the future

Glossary of terms

allele - a variant form of a particular gene
autosomal - non sex chromosome
CNV - copy number variation ( repeats )
CRISPR - a new technology which provides the capability to modify DNA in cells
complex trait - a trait caused by more than one gene and possibly environmental factors also
exome - refers to the protein encoding regions of DNA
epigenetics - refers to modifications the DNA on top of the primary sequence ( for example: DNA methylation or histone modification )
gene - a section of DNA that codes for a specific biological product - usually a protein
genotype - the DNA / genetic material or an organism
GWAS - a type of scientific study where gene sequences of control group and experimental group are compared to determine correlations between genotype and phenotype variations
indel - insertion or deletion
mutation - a relatively rare genetic variation , in less than 1% of the population
nucleotides - A, T, C, G - the rungs of the DNA ladder
phenotype - the physical appearance of an organism - the result of genotype and environment
sex chromosome - chromosome that determines sex ( X or Y chromosome )
SNP/SNV - single nucleotide polymorphism/variant
SV - structural variant , such as insertions, deletions, duplications

Other web sites:

NHGRI GWAS Catalog - a catalog of Genome Wide Association studies on multi-gene diseases and traits
IGSR - The International Genome Sample Resource
COSMIC - the Catalogue Of Somatic Mutations In Cancer
OMIM - comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily
PharmGKB - a web site for pharmacogenetics
100,000 Genomes Project - project to sequence the genomes of 100,000 patients in the UK
dbGaP - database of Genotypes and Phenotypes

About the author

Steve Johnson - independent researcher and scientist
Formal education in math, computer science, physics, chemistry, molecular biology and genetics, etc.
Interested in genomics as a way to prevent and/or treat disease

Helping people understand their personal genomic data

Why you should get your DNA analyzed:

Where can I get my genome analyzed direct-to-consumer (without going through a doctor) and what is the cost?

How can I analyze my genome data myself?

The human genome summary:

Some diseases caused by variants in a single gene (monogenic)

Some diseases caused by variants in more than one gene (polygenic)

Traits determined by variants in multiple genes (polygenic)

What are some applications of personal genomics?

Glossary of terms

Other web sites:

About the author

Email address: info@geneuniverse.com