Norwich Embark Reports

Introdction

As part of a project to study the genetic diversity of Norwich terriers, I am using the Embark DNA test. Embark is a consumer canine DNA health panel testing company. Embark provides a report listing any disease mutations that they find, DNA information on coat color, and much more. In addition Embark also makes available the values of the raw DNA that they genotype (sample) - approximately 200,000 values. This raw data is what I want for my diversity project.

So far I have tested 36 Norwich.

Although I am primarily interested in the raw DNA, it makes sense to look at the Embark reports. Below is a summary of the Embark reports, with some commentary. (The summary follows the order of an Embark report. If you have never seen an Embark report, one can be found here.) This information may change as I test more Norwich and learn more. I am expecting this to be a multi-year project, as I need the raw DNA of a lot of Norwich to get accurate genetic diversity information.

Last updated 20180914.

A genetics primer

This section can be read later if you just want to compare a report to the summary. But if something is unclear, you might want to come back and read this section.

Gregor Mendel in his 1865 paper observed that pea plants inherit traits by way of discrete "units of inheritance", subsequently called "genes". He described "dominant" and "recessive" modes of inheritance. The importance of Mendel's work did not gain wide understanding until 1900 (after his death) when scientists rediscovered his research. In 1911, scientists realized that these genes must be on chromosomes. We now know that chromosomes always come in pairs - one inherited from the mother; the other from the father. Dogs have 39 pairs of chromosomes, for a total of 78 chromosomes. (Humans have 23 pairs.)

In 1953, Watson and Crick building on years of work by other scientists, determined the structure of chromosomes, by then known by their chemical name - deoxyribonucleic acid (DNA). Each chromosome is made up of two strings (shaped in a double-helix pattern) of four organic molecules that have the initials A, T, C, and G. The organic molecule A (on one string) always pairs with T (on the other string), and C always pairs with G. Dogs have approximately 2.8 billion of these pairs. (Humans have approximately 3.2 billion.)

Between any two dogs, only about 0.1 percent of the 2.8 pairs differ. These differences (mutations) in DNA fall into several categories. The most common are single nucleotide polymorphisms (SNPs), which are just changes in a particular pair. All the DNA around the SNP is the same, yet at that particular position an A-T pair has switched to a C-G pair (or vice versa). Another common class of mutations are "indels" - either insertions (I) or deletions (D) of short (or long) stretch of DNA pairs.

It currently costs approximately $2000 to sequence (read) all 2.8 billion pairs of a dog's DNA (genome). ($1000 for humans, as there is a much more competitive market for sequencing human DNA.) A cheaper technology just looks at a sample of DNA at particular positions, this is called genotyping. Genotyping is part of what Embark does, reporting back approximately 200,000 SNP positions.

Instead of reporting "A-T and C-G" (one from the mother and one from the father), it is simpler to just report AC ... or AG or TC or TG.

Wolfiness, Weight, Age

Wolfiness

Embark says that their "wolfiness" calculation is the percentage of ancestoral wolf genes that are in the dog. I have not figured out exactly what Embark is calculating. I have seem a range of values for Norwich, from 0.3 to 1.8 percent, normally distributed centered somewhere around 0.8 percent. Wolfiness does not seem to correlate with prey drive. (A high prey-drive Norfolk that I tested had wolfiness of 0.0 percent!)

References:

Comparison of village dog and wolf genomes highlights the pivotal role of the neural crest in dog domestication, Pendleton et al., biorxiv, 2018.

The genomic signature of dog domestication reveals adaptation to a starch-rich diet, Axelsson et al., Nature, 2013.

Weight

Approximately 20 SNP locations predict the size (weight) of a dog. (In humans, it is known that over a hundred genes affect height.)

Reference:

A Simple Genetic Architecture Underlies Morphological Variation in Dogs, Boycko et al., PLOS Biology, 2010.

Age

I suspect that Embark is calculating human-age equivalent of a dog using the length of the telomeres at the ends of the chromosomes. A telomere is a region of repetitive sequences of pairs at each end of a chromosome; length of the repetitive sequence seems to corrolate with age.

Maternal Haplotypes

A maternal haplogroup or haplotype is a sequence of DNA that is always passed down from a mother and exists in mitochondrial DNA. A haplotype is a specific subtype of a haplogroup. A maternal haplogroup or haplotype allows one to trace the maternal lineage of any dog going back thousands of years. This kind of information is frequently used in genetic geneology.

So far I have found four maternal haplotypes in Norwich. Of the 36 Norwich that I have tested so far

num Haplogroup Haplotype
11A1a A17
10B1 B1b
7B1 B1/13
8C2 C3/14

Paternal Haplotype

The paternal haplotype is a sequence of DNA that exists on a male's Y chromosome. (So it only exists on male dogs.) It allows one to trace the paternal lineage of any dog going back thousands of years. So far I have only seen one paternal haplogype in Norwich

Haplogroup Haplotype
A1a H1a.2

Traits

Coat Color

There are two pigments that make up dog coat color: eumelanin (black) and phaeomelanin (red) - it is the combination of these two pigments in various ways that make up all the shades of coat color. Much about coat color is still not known, and this is still an active area of scientific research. Since canine coat color was studied prior to the canine genome being sequenced, the genes involved were given descriptive names: A (agouti), E (mask, grizzle, recessive red), D (dilute, blue). And instead of the word "gene" sometime the word "locus" is used. For more about coat color, see http://www.doggenetics.co.uk.

Most Norwich breeders know that black-and-tan coat color is recessive to red coat color.

When considering the genetics of coat color for Norwich, the first thing to look at is the A locus. Norwich have two A locus variants (alleles), ay (red) and at (black-and-tan). Black-and-tan is recessive to red. So

Some of the reds may have black markings or be grizzle. This is caused by modifier genes, not all of which have been discovered.

One of these is the E locus. I have seen three E locus alleles in Norwich - Em (mask), E (black), e (red). These can modify a red Norwich. Em is dominant to E, which is dominant to e. I am not sure what each does, but have listed the names commonly given to them.

Of the 36 Norwich that I have tested so far

numA locusE locusPhenotype
3ayayEmEmRed + ??
5ayayEmERed + ??
2ayayEERed + ??
1ayayEeRed + ??
3ayatEmEmRed + ??
8ayatEmERed + ??
1ayatEmeRed + ??
6ayatEERed + ??
2atatEmEmBlank and Tan
4atatEmEBlank and Tan
1atatEEBlank and Tan

If anyone has better descriptors for the color phenotype for these genetic combinations, I would be very interested to learn more.

So far I have seen four Norwich that are Dd (carry the recessive d dilution allele) on the D locus; most Norwich are DD. I understand that dd causes a black-and-tan (atat) to be blue-tinted; while on a Norwich with the ay allele, dd causes a light wheaten color.

All Norwich that I have tested so far have B Locus values of BB and K Locus values of kyky, meaning that these values are fixed in Norwich.

Other Coat Traits

Furnishings, Shedding, and Curly Coat all seem to be fixed in Norwich, being FF (F being an allele name), CC, and CC respectively.

However Long Haircoat is not. The FGF5 gene determines the length of a dog's hair. A recessive mutation at a particular spot in this gene can cause a Norwich to be a fluffy. At the particular position in question, most Norwich are GG and have a normal coat. However if a Norwich has a TT at this position then it will be a fluffy, and if GT then it is called a fluffy carrier.

Of the 36 Norwich that I have tested so far

Other Body Features

Brachycephaly - The BMP3 gene affects snout length, with the A allele causing a shorter snout. There are at least four other genes that affect snout length.

Of the 36 Norwich that I have tested so far

6 AA
20AC
10CC

Reference:

[Schoenebeck 2012]Variation of BMP3 Contributes to Dog Breed Skull Diversity, Schoenebck et al., PLOS Genetics, 2012.

Natural Bobtail seems to be fixed in Norwich with all Norwich being CC.

Hind Dewclaws - a recessive T mutation (meaning that two copies of the T allele must be present) in the LMBR1 gene should cause a hind dewclaw.

Of the 36 Norwich that I have tested so far

21 CC
15CT
0TT

Reference:

Canine Polydactyl Mutations With Heterogeneous Origin in the Conserved Intronic Sequence of LMBR1, Park et al., Genetics, 2008.

Body Size

IGF1, IGF1R, STC2, GFR (E195K), and GHR (P177L) are the scientific names given to certain genes.

Body Size IGF1 - Most Norwich are II, although I have seen one NN and seven NI. The I allele is associate with smaller size.

Reference:

A Single IGF1 Allele Is a Major Determinant of Small Size in DogsSutter et al., Science, 2007.

Body Size IGF1R - Most Norwich are GG, although I have seen three GA. The A allele is associate with smaller size.

Reference:

The insulin-like growth factor 1 receptor (IGF1R) contributes to reduced size in dogs, Hoopes et al., Mamm Genome, 2012.

Body Size STC2 - Most Norwich are TA, although I have seen nine TT and eight AA. The A allele is associate with smaller size.

Body Size GHR (E195K) - Most Norwich are AA, although I have seen seven GA. The A allele is associate with smaller size.

Body Size GHR (P177L) - This seems to be fixed in Norwich at CC. The T allele is associate with smaller size.

Reference:

Derived variants at six genes explain nearly half of size reduction in dog breeds, Rimbault et al., Genome Res., 2013.

Performance

Altitude Adaptation - The seems to be fixed in Norwich at GG.

Genetic Diversity

Inbreeding Coefficient - Embark is calculating the ratio of the total "runs of homozygosity" (ROH) to the total length of all the chromosomes. I believe they are using ROH of 1 million base pairs. This method is becoming the standard way to calculate genetic diversity using genetic data.

Embark says "The higher the inbreeding coefficient, the more closely related the parents. In general, higher inbreeding coefficients are associated with increased incidence of genetically inherited conditions." I have seen a Norwich as low as 27 percent and one as high as 48 percent. (I actually own both Norwich.) Values so far seem to be uniformly distributed between these two extreme values.

27% (0 percentile)
31% (quarter percentile)
37% (half percentile)
41% (three-quarters percentile)
48% (full percentile)

MHC (Major Histocompatibility Complex

Some scientists believe that a highly diverse MHC means a stronger immune system; however, this is disputed by other scientists. DLA stands for "dog leukocyte antigen" which is an interchangeable term for MHC when talking about dogs. DRB1, DQA1, and DQB1 are specific DNA regions of the MHC.

MHC Class II - DLA DRB1 Diversity

Of the 36 Norwich that I have tested so far

14High Diversity
4Low
18No

MHC Class II - DLA DQA1 and DQB1 Diversity

15High Diversity
0Low
21No

Clinical Traits

ALT - One of the serendipitous findings of this project is that some Norwich carry the clinical mutation for "low normal" ALT values. ALT is a common value on most blood chemistry panels and is known to be a sensitive measure of liver health. A Norwich with one or two of the mutant ALT alleles is likely to have low normal ALT values on a blood chemistry. This is a clinical state, not a disease state.

A rise from a low normal value may still fall in the blood lab's normal range and thus be missed by a veterinarian, when it is in fact saying that something is not right and should be further investigated. This is the first example of personalized medicine for our Norwich.

So far I have seen five Norwich that carry the ALT mutation, one Norwich carries two copies (meaning that they got one copy from their sire and one from their dam), and the other four carry just one copy. Two of these dogs are third cousins. I have also seen one Norfolk that carries one copy of the ALT mutation. I suspect this is an ancestoral mutation.

Reference: Genetic Mapping of Novel Loci Affecting Canine Blood Phenotypes, White et al., PLOS One, 2015.

Health

Embark tests for approximately 160 genetic diseases that have known DNA tests. Of these genetic diseases, so far only two have been found in Norwich: Primary Lens Luxation and Degenerative Myelopathy.

Primary lens luxation (PLL) is a painful, genetic eye disorder that can lead to blindness, and is found in many terrier breeds including Norwich. It typically occurs between 4 and 8 years of age.

Degenative Myelopathy (DM) is a late-onset neuromuscular disorder, that is frequently mistaken for a spinal cord injury. Dog with DM have paralysis that begins with the hind legs and the paralysis slowly moves towards the head.

In the population of Norwich that I have Embark tested, there is one Norwich who is a PLL-carrier (currently listed on the OFA web site), and one who is a DM-carrier (not listed on the OFA web site).