Example. The whole genome example's CYP2D6 Structural Analysis, from a public genome in the 1000 Genomes Project, so you can see what yours will show. Get yours
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How we reached your CYP2D6 result
Everything we measured from the reads in your CRAM file, and how it led to your result. Start with the summary; each step below shows the evidence behind it.
Your result
GRCh38*2/*2x2
Ultrarapid Metabolizer
Your CYP2D6 enzyme is more active than usual.
Metabolizer status, set by your activity score (3)
- Poor0
- Intermediate0.25 to 1
- Normal1.25 to 2.25
- Ultrarapidyours: 3
How sure we are
Confidence: DecisiveNo other pairing of CYP2D6 alleles fit your reads closely enough for us to weigh it against this one.
What measuring the structure changed
Your VCF alone showed *2/*2 (Normal Metabolizer). Your reads show *2/*2x2: one chromosome carries two copies of *2. That makes you an Ultrarapid Metabolizer instead, which changes guidance for 28 of your medications.
The 28 medications
- Amitriptyline
- Amphetamine
- Aripiprazole
- Brexpiprazole
- Clomipramine
- Clozapine
- Codeine
- Desipramine
- Doxepin
- Eliglustat
- Fluvoxamine
- Haloperidol
- Hydrocodone
- Imipramine
- Meclizine
- Metoprolol
- Nortriptyline
- Oliceridine
- Ondansetron
- Paroxetine
- Pimozide
- Risperidone
- Tramadol
- Trimipramine
- Tropisetron
- Venlafaxine
- Vortioxetine
- Zuclopenthixol
Your gene copies
You have three copies of CYP2D6
Most people have two, one on each of their two chromosome 22s (one from each parent). On yours, one chromosome carries two copies of *2. A copy can be missing, doubled, or fused with CYP2D6's inactive neighbour, CYP2D7.
Chromosome 22from one parent
Chromosome 22from the other parent
-
CYP2D62D6
*2
Normal function
Activity 1
Key change: 4181G>C
How your copies add up
*21*21*21 activity score 3
Each copy adds its activity: 1 for a copy that works normally, less for one that works less well, 0 for one that doesn't work or isn't there. The total is your activity score, which sets your metabolizer status.
Copy number
Your reads measure 3.0 copies at CYP2D6
Each copy of a stretch of DNA adds reads. We compare the reads at CYP2D6 with 42 regions elsewhere in your genome that everyone has two copies of: about 41 reads cover each spot there.
That's clearly more than the two most people have: most of the control regions measure 1.9 to 2.1.
CYP2D6 and CYP2D7 copies together, from read depth alone
Most people have 4, two of each. Your reads measured 5.3; on read depth alone, 5 is the most likely (58%). Your result has 5, and the variants and CYP2D6-or-CYP2D7 sites below agree.
| Region | Copies | Reads per spot |
|---|---|---|
| CYP2D6 | 3.03 | 63.2 |
| Spacer | 2.32 | 45.6 |
| CYP2D7 | 2.26 | 47.4 |
| Control regions (middle) | 2.03 |
| 4 copies | 2% |
|---|---|
| 5 copies | 58% |
| 6 copies | 33% |
| 7 copies | 6% |
CYP2D6 or CYP2D7
No hybrid copies: your reads stay CYP2D6 along the whole gene
CYP2D6 and CYP2D7 are almost identical, but differ at about 140 places. At each one, your reads show whether they came from CYP2D6 or CYP2D7. With no hybrid copy, the count stays level along the gene.
Up the side: CYP2D6-like copies the reads imply, out of the 5 CYP2D6 and CYP2D7 copies your result has. Single sites scatter; the teal line shows the level they settle at.
No copy switches to CYP2D7 along the gene.
140 sites where CYP2D6 and CYP2D7 differ were read.
The variants
The two changes behind your result
Star alleles are named by the DNA changes they carry, compared with *1. Here is every change that defines your alleles or told your result apart from the others: which of your copies carry it, and how many of your reads show it. If one of three copies carries a change, about a third of your reads should show it; the tick on each bar marks what your result predicts. Open any change to see its reads.
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2851C>T R296C
rs16947 · Exon 6 · GRCh38 42,127,941
A common change (R296C) found on *2 and many other alleles. On its own it has little effect.
Your copies
Carried by *2
68 of 68 read pairs (100%)
All three of your copies carry it, so your result predicts 100% (the tick on the bar)
See the 76 reads at 2851C>T
71T, the change
Each bar is one read, about 150 DNA letters, lined up on the genome; the line down the middle is the variant. 76 reads cover it. The counts are the 71 reads we used, from the 68 read pairs counted above: when both reads of a pair cross this spot, each is drawn. 5 faded ones were set aside (duplicates or uncertain alignments).
-
4181G>C S486T
rs1135840 · Exon 9 · GRCh38 42,126,611
A common change (S486T) found on most alleles other than *1. On its own it has no known effect.
Your copies
Carried by *2
54 of 54 read pairs (100%)
All three of your copies carry it, so your result predicts 100% (the tick on the bar)
See the 72 reads at 4181G>C
65C, the change
Each bar is one read, about 150 DNA letters, lined up on the genome; the line down the middle is the variant. 72 reads cover it. The counts are the 65 reads we used, from the 54 read pairs counted above: when both reads of a pair cross this spot, each is drawn. 7 faded ones were set aside (duplicates or uncertain alignments).
About your file
What we read
- Genome build
- GRCh38
- Reads per spot
- about 41 in the control regions, 55 around CYP2D6 (we need at least 20)
- Control regions
- 42
- Reads in proper pairs
- 98%
- Region read
- chr22:42,096,498-42,160,902
- CYP2D6
- chr22:42,126,499-42,130,898
- Caller version
- 1.0
Words on this page
A short glossary
- Read
- A short piece of your DNA, about 150 letters, as the sequencer read it. Your file has millions; we use the ones around CYP2D6.
- Read pair
- The sequencer reads both ends of each DNA piece. We count a pair once.
- Star allele
- A named version of CYP2D6, such as *1 or *4, defined by the changes it carries.
- Copy number
- How many copies of CYP2D6 you have. Usually two; some people have one, three or more.
- CYP2D7 and hybrids
- CYP2D7 is CYP2D6's inactive neighbour. A hybrid copy is part CYP2D6 and part CYP2D7, and usually doesn't work.
- Spacer
- The stretch of DNA between CYP2D6 and CYP2D7. An extra copy of CYP2D6 brings an extra copy of it too, so it helps confirm a duplication.
- Activity score
- The sum of what each of your CYP2D6 copies does: 1 for a copy that works normally, less for one that works less well, 0 for one that doesn't work.
- Metabolizer status
- Poor, intermediate, normal or ultrarapid, set by your activity score. Medication guidance is written for each status.