A long line of previous work has already established non Prnp
-linked genetic modifiers as important determinants of incubation time 
. As it is customary that the initial scientific rationale for such work is provided by analyses of heritability, it is slightly ironic that the estimation of heritability for human prion phenotypes has only very recently been possible 
. One factor precluding heritability analyses of vCJD, a future potential public health risk, is its low recurrence rate among nuclear families; there has been just one case of vCJD recurring in a family (Source: European Centre for Disease Prevention).
The heritability of age at onset and death for the human inherited
TSE form was recently determined to be 0.55 (95% CI 0.35–0.75) 
. This value is comparable to our own estimates which derive from a related phenotype and are the first to be reported for an acquired
TSE (h2narrow sense
0.3 to 0.6). As in 
, our estimates exclude direct effects from Prnp
and suggest a cumulatively modest contribution of non-Prnp
effects. We demonstrate that they may nevertheless outweigh those of the only known major locus, in response to varying the parameters explored by this study.
Our QTL data, only partially justifies our findings in relation to heritability, thus we acknowledge and draw further attention to the many possible sources of bias on which such estimates may rely 
. Additionally further biases may result due to the relatively small proportion of the currently available BXD strains sampled in the study, irrespective of any phenotypic similarity observed between BXDs and F2s across traits (Pearson's r
0.049). In this instance, the use of the expanded BXD set now available was not possible, but may well have resolved such curiosities as a recurrent but unconfirmed locus on chromosome 10 for BSE ic
(BXD), Me7 ip
(F2), and BSE ip
(F2). Such patterns may not occur randomly and may actually reflect additional complexity at these loci. Evidence that the distribution of BXD and F2 QTLs in our data is non-random derives from the fact that:
- A combination of stringently employed mapping and meta-analytical methodologies have yielded many pre-existing QTLs known to be involved in controlling prion incubation times.
- There are a high number of F2 QTLs in relation to the much smaller hypothesis region tested (9 F2 QTLs were identified within the 27 marker loci tested, whereas 12 BXD QTLs were identified across 3795 tested marker loci). The F2 number is significantly higher than a priori expectations based on extrapolated BXD data (PYates corrected χ2<<0.0001) and argues that the methodological procedures in the BXD analysis offer sufficient protection against Type 1 error in this study. This implies enrichment for genuine QTLs in BXD and F2 data as well as further complexity in the mechanism underlying these QTLs. That previously reported QTLs were detected by this study goes some way to reaffirming the validity of a novel suggestive (p<8×10−4) locus on chromosome 1 (35–62 cM) and a significant (p<2.6×10−5) locus on chromosome 18 (4–17 cM).
F2 mapping was, by itself, able to reproduce a locus on chromosome 2 specific to BSE ic
that reached the genomewide threshold for suggestive significance (p
0.63). That this locus did not survive the subsequent random effects
meta-analysis procedure merely emphasises the heterogeneity between the BXD and F2 estimates and does not contradict the initial evidence suggesting linkage at this region. The chromosome 2 QTL lies approximately 50 centiMorgans (cM) upstream of Prnp
(located at 75 cM). Independence of the chromosome 2 locus from Prnp is
assumed. Among the loci identified for ic
transmissions are a number of familiar linkage regions, (corresponding to regions of chromosomes 2, 4, and 11) previously linked to this route 
We are the first study to attempt to quantify the genetic basis of aetiological overlap governing different routes and agents. highlights the potential for strong overlap effects, even when traits differ simultaneously by host adaptation, route and agent. The caveat is that strong effects of route and agent on genetic influence, suggest that QTLs identified in one study cannot necessarily be extrapolated to transmission models based on different combinations of agent and route. Thus, while it may be too tempting to resist extrapolating previously reported data to the oral route (a route more relevant to the transmission vCJD) our data suggest that doing so may blur the little that we understand of the genetic processes regulating the transmission of vCJD and the potential risk to public health that they may represent. This is because even the strongest correlating traits in our study do not share more than 70% of genetic influences in common, while our lowest estimates suggest that the dissimilarity between transmissions can mean just 50% overlap or less, even between transmissions using a common administration route ().
The overall implication is that any lingering uncertainty about the identity of risk variants in vCJD may be best tackled using mapping strategies that specifically target the more relevant oral route. Reassuringly, suggests some portion of genetic influence may be common to all traits. The emphatic nature of the meta-analysis result and other prior linkage evidence makes the chromosome 11 locus one prime candidate for mediating such a role. Meta-analysis also highlights a number of other significant candidate regions, which are summarised in . Trait-specific QTL effects of varying significance were found on chromosomes 1, 2, 4, 6 and 18, after the merging of BXD and F2 data.
Our data represent the third independent report of a distinct TSE locus on chromosome 2 (). The linkage region overlaps with previous QTLs identified in 
. Other QTLs located at the distal end of chromosome 2 have been identified by Lloyd et al 
. It is not clear to what extent these may be specific to the CAST/Ei x NZW/OlaHsd background in which they occurred. Interestingly one of the regions of Lloyd et al spans loci of both the prion protein (Prnp
) and that of its paralogue Doppel (Prnd
), although sequence symmetry between progenitor strains at this locus rules out effects from within either gene. We are the third group to independently report the existence of QTLs for prion disease on chromosome 11. Previous studies have already established this chromosome as a good linkage candidate. Crucially however, our meta-analysis data attaches empirical significance to this locus. This suggests wider involvement across a variety of other transmission types not characterised previously. Candidate-based explorations of the region have so far failed to reveal the origins of such effects 
Summary of QTL intervals affecting TSE transmission by study (3a) and by genetic background (3b).
Lloyd et al 
( and ) observed similar genetic factors to those found in a previous investigation of the ic
confirming the veracity of these loci. This result is perhaps not surprising given that each study uses the same genetic cross (NZW/Hsd and Cast/Ei) and only the TSE strain used (both host-adapted) varies. Moreno et al 
and Manolakou et al 
employ prion agents at different stages of host-adaptation. This may account for individual discrepancies between these results (in addition to methodological and environmental/epigenetic considerations) although, common regions on chromosomes 4 and 8 indicate a broader similarity between their findings.
Summary of TSE linkage findings to date.
Previous studies show a bias towards C57-derived genetic backgrounds. Of the QTLs shown in we see that regions on chromosomes 2, 6 and 11 have the most general influence across varied genetic backgrounds. The chromosome 11 has already been mapped in two non C57-derived backgrounds, while loci on chromosomes 2 and 6 have been identified in the NZW/Hsd and Cast/Ei genetic cross.
A recent GWA study of human TSEs draws attention to novel common variants associated with clinical phenotypes, implicating genes such as STMN2
. In addition, previously uncharacterised variants have also been discovered within PRNP 
. The study identified two loci of genome-wide importance, one in strong LD with the major locus at codon 129 and another found in the intergenic region between RARB
. The other genome-wide significant finding in this study highlighted a locus for orally acquired TSEs (vCJD and Kuru), using meta-analysis. Underlying genetic heterogeneity found between TSE categories in this study mirrors our own findings. We assume this to reflect that factors such as agent, dose and route also have an important role in aetiological determinism and its corresponding genetic framework.
The low recurrence rate of familial vCJD precludes studies of human linkage, in which rare disease loci may be detected by virtue of their increased occurrence among affected relatives. This and the low global incidence of vCJD, means increasingly-available next-generation sequencing methods cannot yet be fully exploited to define the possible contribution of rare variants to the TSEs. Recent progress made, across psychiatry in particular, has helped to demonstrate the pathogenic potential of this variant class 
. Meanwhile, the continued application of linkage studies to murine proxies must continue in order to provide further cues for fine-mapping and positional cloning work. Gene targets identified by such approaches can advance human prion research by exploiting synteny between murine and human biological systems. QTL mapping in Heterogeneous Stock mice offers superior resolution to the RI approach and use of this genetic resource has the potential to expedite the search for QTLs by reducing the size of candidate regions to relatively few genes. Such approaches have been applied to great effect and have heralded the first wave of gene candidates and confirmed trait loci 
to derive from murine QTL mapping of the TSEs.
Our findings concur with previous reports linking QTLs on chromosomes 2, 4, 6 with TSE incubation time. We also report a novel QTL on chromosome 18. Additionally our results enable us to extrapolate from a previous linkage region on chromosome 11 linked with ic
transmissions, to a general effect spanning across ic
routes and natural/host adapted prion agents. The generality of this locus may make it a prime candidate for involvement in the general pathogenesis of TSEs, including vCJD. Our demonstration of the substantial selectively with which host genetics may act across different transmission models suggests that not all QTLs identified using the historically favoured ic
model will feature as strongly for orally acquired TSEs. The enduring aetiological relevance of this route to vCJD contrasts with the apparent decline in the number of cases resulting from blood transfusions 
. Thus a paradigm shift may be warranted to aid the detection of biological effects specific to vCJD. Such reasoning dictates that oral
TSE transmissions should be the next priority for mapping studies of this type.