What is genome particle? Does it refer to "viral genome particle"?

Subfoveal = under the fovea

Fovea :
(anatomy) A slight depression or pit in a bone or organ.
(anatomy) The retinal fovea, or fovea centralis, responsible for sharp central vision.

In this case, it refers to the latter.

Genone particles = bits of DNA.

It doesn't refer to viral genome particle.

Retinal gene therapy in patients with choroideremia: initial findings from a phase 1/2 clinical trial
Original Text
Prof Robert E MacLaren FRCOphth a b c , Markus Groppe PhD a b c, Alun R Barnard PhD a, Charles L Cottriall PhD b, Tanya Tolmachova PhD d, Prof Len Seymour PhD e, K Reed Clark PhD f, Prof Matthew J During FACP g, Prof Frans P M Cremers PhD h, Prof Graeme C M Black FRCOphth i, Prof Andrew J Lotery FRCOphth j, Susan M Downes FRCOphth a b, Prof Andrew R Webster FRCOphth c k, Prof Miguel C Seabra MD d l
Summary
Background
Choroideremia is an X-linked recessive disease that leads to blindness due to mutations in the CHM gene, which encodes the Rab escort protein 1 (REP1). We assessed the effects of retinal gene therapy with an adeno-associated viral (AAV) vector encoding REP1 (AAV.REP1) in patients with this disease.
Methods
In a multicentre clinical trial, six male patients (aged 35—63 years) with choroideremia were administered AAV.REP1 (0·6—1·0×1010 genome particles, subfoveal injection). Visual function tests included best corrected visual acuity, microperimetry, and retinal sensitivity tests for comparison of baseline values with 6 months after surgery. This study is registered with ClinicalTrials.gov, number NCT01461213.
Findings
Despite undergoing retinal detachment, which normally reduces vision, two patients with advanced choroideremia who had low baseline best corrected visual acuity gained 21 letters and 11 letters (more than two and four lines of vision). Four other patients with near normal best corrected visual acuity at baseline recovered to within one to three letters. Mean gain in visual acuity overall was 3·8 letters (SE 4·1). Maximal sensitivity measured with dark-adapted microperimetry increased in the treated eyes from 23·0 dB (SE 1·1) at baseline to 25·3 dB (1·3) after treatment (increase 2·3 dB [95% CI 0·8—3·8]). In all patients, over the 6 months, the increase in retinal sensitivity in the treated eyes (mean 1·7 [SE 1·0]) was correlated with the vector dose administered per mm2 of surviving retina (r=0·82, p=0·04). By contrast, small non-significant reductions (p>0·05) were noted in the control eyes in both maximal sensitivity (—0·8 dB [1·5]) and mean sensitivity (—1·6 dB [0·9]). One patient in whom the vector was not administered to the fovea re-established variable eccentric fixation that included the ectopic island of surviving retinal pigment epithelium that had been exposed to vector.
Interpretation
The initial results of this retinal gene therapy trial are consistent with improved rod and cone function that overcome any negative effects of retinal detachment. These findings lend support to further assessment of gene therapy in the treatment of choroideremia and other diseases, such as age-related macular degeneration, for which intervention should ideally be applied before the onset of retinal thinning.
Funding
UK Department of Health and Wellcome Trust.

The genome particles are administrated along with (associated) an adeno viral vector.

You should then infer that the genome particles don't refer to viral genome particles.

the CHM gene, which encodes the Rab escort protein 1 (REP1).

Stay calm.

Read this:

Quote:

the CHM gene, which encodes the Rab escort protein 1 (REP1).

That's what the CHM gene usually does.

If the gene mutates, you get Choroideremia (recessive disease).

Then they administer a genome particle (bit of DNA) along with an adeno-associated viral vector (not human in my view) in order to restore the basic function of the CMH gene.

No.

You are mixing up stuff, Oristar.

You need to check out some biology notions.

The retinal therapy corrects the CHM gene.

When the disease appears, the REP 1 is not processed properly and it's not it that mutates but the CHM gene.

So, the adeno-associated viral vector (AAV), along with the genome particles correct the CHM gene action processing the REP1.

In this sentence, what encoding REP1? The writer failed to mention it.

Encode
To convert source information into another form.

Encoding
The first stage in the memory process, followed by storage and retrieval, involving processes associated with receiving or briefly registering stimuli through one or more of the senses and modifying that information; a decay process or loss of this information (a type of forgetting) occurs rapidly unless the next two stages, storage and retrieval, are activated.

Phase 0: Pharmacodynamics and Pharmacokinetics
Phase 1: Screening for safety
Phase 2: Establishing the efficacy of the drug, usually against a placebo
Phase 3: Final confirmation of safety and efficacy
Phase 4: Sentry studies during sales

Oristar wrote:

In this sentence, what encoding REP1? The writer failed to mention it.

Again, you need to check out your biology basics. The writer is not a biology professor giving a course.

The sentence is fine by me.

with an adeno-associated viral (AAV) vector encoding REP1

Well, I'm not a grammarian but I think it's part of the adverbial clause:

Quote:

with an adeno-associated viral (AAV) vector encoding REP1

The sentence is fine by me.