The N342S MYLIP polymorphism is associated with high total cholesterol and increased LDL receptor degradation in humans

Probably not a substantial claim: may not pass S3 (load-bearing).

The LXR-MYLIP-LDLR pathway provides a complementary pathway to sterol regulatory element-binding proteins for the feedback inhibition of cholesterol uptake.

“Thus, the LXR-MYLIP-LDLR pathway provides a complementary pathway to sterol regulatory element-binding proteins for the feedback inhibition of cholesterol uptake (4,5).”

• cites [4] sourceSupported
• cites [5] sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

MYLIP is a direct target for regulation by LXR, and its expression is coordinately regulated with the ATP-binding cassette transporter in multiple cell types.

“MYLIP is a direct target for regulation by the nuclear receptor liver X receptor (LXR), and its expression is coordinately regulated with the ATP-binding cassette transporter in multiple cell types (4).”

• cites [4] sourceSupported

May combine two claims.

Expression of Mylip in mouse liver by means of an adenoviral vector dramatically reduces LDLR protein levels and raises LDL-C levels.

“Expression of Mylip in mouse liver by means of an adenoviral vector dramatically reduces LDLR protein levels and raises LDL-C levels (4).”

• cites [4] sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

Combined hyperlipidemia, the simultaneous elevation of both TC and TG levels, is highly common among Mexican individuals (18% incidence).

“Combined hyperlipidemia, the simultaneous elevation of both TC and TG levels, is highly common among Mexican individuals (18% incidence; ref. 13).”

• cites [13] Aguilar-Salinas, 2010, Salud Publica Mex. sourcePartly supported

  The ‘Prevalence of lipid phenotypes’ section (Table IV) reports simultaneous elevation of cholesterol and triglycerides in 18.2% of the surveyed population, supporting the definition and approximate figure. It reports prevalence, not incidence; the latter would require measuring new cases over time. (LLM, conf=0.88)

  Experimental — accuracy not yet measured

May combine two claims.

The expression levels of MYLIP were not significantly different with respect to the rs3757354 genotypes in the fat biopsies of Mexican subjects or in fat or liver biopsies from subjects of mixed European descent.

“It is worth noting that the expression levels of MYLIP were not significantly different with respect to the rs3757354 genotypes in the fat biopsies of Mexican subjects or in fat or liver biopsies from subjects of mixed European descent (6).”

• cites [6] sourceCould not verify

  The section “Genome-Wide Association Mapping in >100,000 Individuals” describes testing SNP–expression correlations in liver and fat, and “Biological Relevance of GWAS Loci” mentions MYLIP. Neither reports MYLIP expression by rs3757354 genotype or the claimed nonsignificant results in Mexican or mixed-European biopsy samples; searches for rs3757354 and those population-specific results found no such passage in our copy. Page numbers were not provided. (LLM, conf=0.72)

  Experimental — accuracy not yet measured

May combine two claims.

The most strongly associated variant in Mexicans, rs9370867, was in strong LD with the GWAS associated variants rs2480 and rs2294261 in the CEU founders with European ancestry and, to a lesser extent, in the Mexican controls (r2 = 0.73 and r2 = 0.49, respectively).

“Importantly, our LD analyses also demonstrated that the most strongly associated variant in Mexicans, rs9370867, was in strong LD with the GWAS associated variants rs2480 (7) and rs2294261 (6) in the CEU founders with European ancestry and, to a lesser extent, in the Mexican controls (r 2 = 0.73 and r 2 = 0.49, respectively; Figure 3).”

• cites [7] sourceCould not verify

  The citation is attached to the identification of rs2294261 as a GWAS-associated variant, not to the citing authors’ own LD analysis. The Results section on secondary genome-wide analysis reports an association at 6p22.3 implicating GMPR or MYLIP, but the passages retrieved by searches for rs2294261, rs2480, and rs9370867 do not identify rs2294261 or establish its GWAS association. No page numbers were available in our copy. (LLM, conf=0.72)

  Experimental — accuracy not yet measured
• cites [6] sourceCould not verify

  Split into 2 atoms — 0 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 2 unverifiable. Expand the claim to see per-atom verdicts.

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing).

The frequency of the Asn (risk) allele varies considerably among populations (0%-60%).

“The frequency of the Asn (risk) allele varies considerably among populations (0%-60%) (10,14).”

• cites [10] sourcePartly supported

  The section ‘Allele frequency distributions within population samples’ reports differences in allele-frequency patterns among the population panels, supporting the general point that frequencies vary. It does not identify an Asn risk allele or give a 0%–60% frequency range for that allele (searched: Asn, risk allele, and 0%–60%). (LLM, conf=0.77)

  Experimental — accuracy not yet measured
• cites [14] sourcePartly supported

  The Disease susceptibility and other quantitative phenotypes section (page unavailable) identifies a risk allele at SH2B3 and reports that its region differs between Europe and East Asia. It does not identify that allele as Asn or give a population-frequency range of 0%–60%, so those specific parts of the claim are unsupported by our copy. (LLM, conf=0.72)

  Experimental — accuracy not yet measured

Classified as probably not a substantial claim.

Patterns of linkage disequilibrium vary among populations with different demographic histories.

“As patterns of linkage disequilibrium (LD) vary among populations with different demographic histories (10), studies in a different population than the discovery population, such as Mexican subjects, can assist in fine-mapping the actual susceptibility variants (i.e., trans-ethnic fine-mapping).”

• cites [10] sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

The estimated error rate for the imputed genotypes in the LD analysis sample was less than 1.3%, based on a leave-one-out approximation.

“The estimated error rate for the imputed genotypes in this sample was less than 1.3%, based on a leave-one-out approximation (24).”

• cites [24] sourcePartly supported

  The Accuracy comparison section (page unavailable) treats discordance with observed genotypes as a surrogate for imputation error rate. Modeling considerations (page unavailable) reports rates below 1.3%, but only for particular methods and SNP subsets in the paper's own samples. It does not establish that rate for the citing paper's LD-analysis sample or describe it as a leave-one-out estimate. (LLM, conf=0.82)

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

After excluding imputed genotypes with low quality score (<0.7), the genotype call rate exceeded 90%, and the estimated error rate based on a leave-one-out approximation was less than 2.5%.

“After excluding imputed genotypes with low quality score (i.e., <0.7), the genotype call rate exceeded 90%, and the estimated error rate based on a leave-one-out approximation was less than 2.5% (24).”

• cites [24] sourceCould not verify

  The Accuracy comparison section describes varying posterior-probability calling thresholds and measuring discordance against observed Illumina genotypes. Our copy does not report results at a 0.7 quality cutoff, a call rate exceeding 90%, or an error estimate below 2.5% based on a leave-one-out approximation (searched: 0.7, 90% call rate, 2.5%, leave-one-out). (LLM, conf=0.76)

  Experimental — accuracy not yet measured

May combine two claims.

In recent GWASs and a GWAS meta-analysis of populations of mixed European descent, there were 3 independent (r2 < 0.3) genome-wide significant signals in the MYLIP region, none of which resides within the MYLIP gene.

“In recent GWASs and a GWAS meta-analysis of populations of mixed European descent (6-8), there were 3 independent (r 2 < 0.3) genome-wide significant signals in the MYLIP region, none of which resides within the MYLIP gene.”

• cites [6] sourcePartly supported

  The Genome-Wide Association Mapping section (page unavailable) reports a meta-analysis of 46 lipid GWASs in people of European descent, and the Biological Relevance section identifies MYLIP as a gene implicated by the study. Our copy does not establish that the MYLIP region had three independent signals with r² < 0.3 or that none lay within the gene. (LLM, conf=0.84)

  Experimental — accuracy not yet measured
• cites [7] sourcePartly supported

  The Results (Secondary genome-wide analysis; page unavailable) report a genome-wide significant association at 6p22.3 implicating GMPR or MYLIP, and say its lead SNP was associated with a lipid measure in a published meta-analysis. Our copy does not establish three independent signals, an r² < 0.3 threshold, or that none of the signals lies within MYLIP. (LLM, conf=0.84)

  Experimental — accuracy not yet measured
• cites [8] sourcePartly supported

  The Results section (MYLIP–GMPR; page unavailable) identifies a genome-wide significant LDL-c association at the MYLIP/GMPR locus and places rs2142672 between the two genes. It does not report three independent signals, establish r² < 0.3 among them, or show that all three lie outside MYLIP; instead, it describes other associated SNPs as correlated with rs2142672. (LLM, conf=0.85)

  Experimental — accuracy not yet measured

Classified as probably not a substantial claim. May combine two claims.

Mexicans descend from a recent mix of Amerindian and European ancestry, which has caused marked differences in allelic frequencies and patterns of LD across their genome.

“Mexicans descend from a recent mix of Amerindian and European ancestry, which has caused marked differences in allelic frequencies and patterns of LD across their genome (19).”

• cites [19] sourcePartly supported

  The Results report substantial Native American and European ancestry in the sampled Mexicans and estimate an average of 8.8 generations since admixture. The paper discusses ancestry-informative allele frequencies and greater LD in Native American populations, but does not establish that admixture caused marked differences in allele frequencies and LD patterns across Mexicans’ genomes. No page numbers are available in our copy. (LLM, conf=0.85)

  Experimental — accuracy not yet measured

May combine two claims.

The pairwise LD and the allele frequency of N342S are significantly different between European and Mexican populations.

“Accordingly, the pairwise LD and the allele frequency of N342S are significantly different between European and Mexican populations (10).”

• cites [10] sourceCould not verify

  The paper discusses pairwise linkage disequilibrium and allele-frequency differences among its analysis panels (sections on LD properties and population differentiation; page unavailable). Searches for N342S and for a European–Mexican comparison found no passage reporting the claimed differences or their statistical significance. (LLM, conf=0.76)

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

A total of 14,942 probesets passed quality control procedures, of which only the MYLIP probesets (n = 3) were used in the cis-eQTL analysis.

“A total of 14,942 probesets passed quality control procedures (25), of which only the MYLIP probesets (n = 3) were used in the cis-eQTL analysis.”

• cites [25] sourceSupported

Classified as probably not a substantial claim.

Studies in a different population than the discovery population, such as Mexican subjects, can assist in fine-mapping the actual susceptibility variants.

“As patterns of linkage disequilibrium (LD) vary among populations with different demographic histories (10), studies in a different population than the discovery population, such as Mexican subjects, can assist in fine-mapping the actual susceptibility variants (i.e., trans-ethnic fine-mapping).”

• cites [10] sourceSupported

May combine two claims.

The adjusted means of total cholesterol by rs9370867 genotype were 5.49 mmol/l for Asn/Asn homozygotes, 5.31 mmol/l for Asn/Ser heterozygotes, and 5.20 mmol/l for Ser/Ser homozygotes.

“The adjusted means of TC by genotype were 5.49 mmol/l for the Asn/Asn homozygotes, 5.31 mmol/l for the Asn/Ser heterozygotes, and 5.20 mmol/l for the Ser/Ser homozygotes (Table 2).”

May combine two claims.

The Asn-encoding allele (N342) was associated with more potent LDLR degradation and decreased LDL uptake.

“Functional characterization showed that the Asn-encoding allele was associated with more potent LDLR degradation and decreased LDL uptake.”

May combine two claims.

Regarding the upstream GWAS signal detected by rs3757354, another SNP in LD with it, rs2327949, was identified and was slightly more significant in the Mexican dyslipidemic study sample.

“Regarding the upstream GWAS signal detected by the SNP rs3757354, we identified another SNP in LD with it, rs2327949, which was slightly more significant in the Mexican dyslipidemic study sample.”

May combine two claims.

We did not observe a greater burden of rare and low-frequency variants in either tail of the LDL distribution or detect any rare coding mutations in the Mexican FH patients or hypercholesterolemic probands.

“We did not observe a greater burden of rare and low-frequency variants in either tail of the LDL distribution or detect any rare coding mutations in the Mexican FH patients or hypercholesterolemic probands.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Only about one-third of the total sample size was available for the analysis of rs9370867 (34,733 of 100,000) versus 95,443 available for rs2294261.

“and only about one-third of the total sample size was available for the analysis of rs9370867 (34,733 of 100,000) versus 95,443 available for rs2294261.”

May combine two claims.

The Mexican population has an increased predisposition to combined hyperlipidemia and ASCVD.

“several epidemiological studies have clearly demonstrated that the Mexican population has an increased predisposition to combined hyperlipidemia and ASCVD (11).”

• cites [11] sourceNot checked — no full text of the source

May combine two claims.

In a Mexican population, the nonsynonymous SNP rs9370867, encoding N342S, is an underlying functional variant associated with high total cholesterol and accounts for one of the previous significant GWAS signals.

“Our analysis revealed that in a Mexican population, the nonsynonymous SNP rs9370867, which encodes the N342S amino acid substitution, is an underlying functional variant that was associated with high total cholesterol and accounted for one of the previous significant GWAS signals.”

Classified as probably not a substantial claim.

We examined whether the association results are independent of the top signal rs9370867 by including the minor allele counts (0-2) of rs9370867 as a covariate in the regression analyses.

“We also examined whether the association results are independent of the top signal rs9370867 by including the minor allele counts (i.e., 0-2) of rs9370867 as a covariate in the regression analyses as described above.”

May combine two claims.

The intrinsic E3 ligase activity of S342 MYLIP and its ability to autoubiquitinate is intact.

“These data indicate that the intrinsic E3 ligase activity of S342 MYLIP and, consequently, its ability to autoubiquitinate is indeed intact.”

May combine two claims.

A predicted consequence of the reduction in MYLIP activity in vivo is enhanced expression of LDLR and subsequent uptake of circulating LDL particles, resulting in lower plasma cholesterol levels.

“A predicted consequence of this reduction in MYLIP activity in vivo is enhanced expression of LDLR and subsequent uptake of circulating LDL particles, thus resulting in lower plasma cholesterol levels.”

• AssumptionRests on an assumption: The in vitro effects of MYLIP variants on LDLR degradation reflect in vivo effects on plasma cholesterol.

Probably not a substantial claim: may not pass S3 (load-bearing).

To account for genotype uncertainty, a larger sample size was used in the LD analyses of Mexicans (240 chromosomes, versus 120 available for the CEU sample).

“Hence, to account for this genotype uncertainty, we used a larger sample size in the LD analyses of Mexicans (240 chromosomes, versus 120 available for the CEU sample).”

Classified as probably not a substantial claim.

To correct for multiple testing, the analysis adjusted for the number of independent SNPs (r2 < 0.8) in the region (n = 35) analyzed with 2 traits (TC and non-HDL-C), resulting in Bonferroni correction for 70 independent tests (P ≤ 7.2 × 10-04).

“To correct for multiple testing, we adjusted for the number of independent SNPs (r 2 < 0.8) in the region (n = 35) that we analyzed with 2 traits (TC and non-HDL-C), resulting in Bonferroni correction for 70 independent tests (P ≤ 7.2 × 10 -04 ).”

May combine two claims.

The 72 SNPs analyzed tagged and captured 100% and 94% of the genetic variation with MAF 1% or greater and r2 > 0.8 in the HapMap MEX and CEU samples, respectively.

“Furthermore, the 72 SNPs we analyzed tagged and captured 100% and 94% of the genetic variation with MAF 1% or greater and r 2 > 0.8 in the HapMap MEX and CEU samples, respectively.”

Classified as probably not a substantial claim.

2-sided P values surpassing the Bonferroni multiple-comparison correction threshold for 70 independent tests (P ≤ 7.2 × 10-04) were considered significant.

“2-sided P values surpassing the Bonferroni multiple-comparison correction threshold for 70 independent tests (P ≤ 7.2 × 10 -04 ) were considered significant.”

Probably not a substantial claim: may not pass S3 (load-bearing).

To adjust for the admixed Mexican ancestry, IA estimates were used as a covariate in the regression analyses.

“To adjust for the admixed Mexican ancestry, IA estimates were used as a covariate in the regression analyses (see Supplemental Methods).”

Probably not a substantial claim: may not pass S3 (load-bearing).

The regression models of the TC and non-HDL-C traits were adjusted for hypertriglyceridemia affection status in order to correct for the sampling variable.

“The regression models of the TC and non-HDL-C traits were adjusted for hypertriglyceridemia affection status in order to correct for the sampling variable.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

All SNPs were in Hardy-Weinberg equilibrium (P > 0.05) in the Mexican controls and had a genotyping call rate greater than 95%, with the 34 tag SNPs exhibiting a genotyping call rate greater than 98%.

“All SNPs were in Hardy-Weinberg equilibrium (P > 0.05) in the Mexican controls and had a genotyping call rate greater than 95%, with the 34 tag SNPs exhibiting a genotyping call rate greater than 98%.”

Probably not a substantial claim: may not pass S3 (load-bearing).

The likelihood was maximized using an expectation-maximization algorithm, as implemented in SNPTEST version 2.1.1 software, in order to account for genotype uncertainty in the regression analyses of the imputed SNPs.

“The likelihood was maximized using an expectation-maximization algorithm, as implemented in SNPTEST version 2.1.1 software (26), in order to account for genotype uncertainty in the regression analyses of the imputed SNPs.”

• cites [26] sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

Novel variants that were not present in dbSNP build 130 were sequenced on both strands.

“Novel variants that were not present in the dbSNP build 130 were sequenced on both strands.”

May combine two claims.

I202 and V339 are not critical for MYLIP-induced degradation of LDLR.

“These observations suggest that I202 and V339 are not critical for MYLIP-induced degradation of LDLR.”

May combine two claims.

The presence of a Ser at position 342 resulted in attenuated ubiquitination of LDLR, increased expression of surface LDLR, and a concomitant increase in LDL uptake.

“The presence of a Ser at this site resulted in attenuated ubiquitination of LDLR, increased expression of surface LDLR, and a concomitant increase in LDL uptake.”

Classified as probably not a substantial claim.

To assure that the associations were not confounded by population admixture, the test of association included adjustment for ancestry estimates as a covariate.

“To assure that the associations were not confounded by population admixture, we also performed the test of association including adjustment for ancestry estimates as a covariate.”

Classified as probably not a substantial claim. May combine two claims.

Subjects with trait levels more than 4 SD from the mean or on lipid-lowering therapy at the time of the blood drawing were excluded from the quantitative analyses.

“Subjects with trait levels more than 4 SD from the mean or on lipid-lowering therapy at the time of the blood drawing were excluded from the quantitative analyses.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

All 38 imputed SNPs exhibited good imputation quality (certainty >92%) and were in Hardy-Weinberg equilibrium (P > 0.1) in the Mexican controls.

“All 38 imputed SNPs exhibited good imputation quality (certainty, >92%) and were in Hardy-Weinberg equilibrium (P > 0.1) in the Mexican controls.”

Probably not a substantial claim: may not pass S3 (load-bearing).

For subjects with TG in excess of 4.5 mmol/l (400 mg/dl; n = 947), LDL-C values were not calculated because the Friedewald equation cannot be reliably used with such high TG values.

“However, for subjects with TG in excess of 4.5 mmol/l (400 mg/dl; n = 947), LDL-C values were not calculated, as the Friedewald equation cannot be reliably used with such high TG values (22).”

• cites [22] sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

Most variants identified in GWASs reside outside of coding sequence.

“As yet, the function of most variants identified in GWASs is unknown, and most of these variants reside outside of coding sequence (9).”

• cites [9] McCarthy, 2008, Nat Rev Genet. sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

DNA sequencing was used to verify mutant constructs.

“DNA sequencing was used to verify mutant constructs.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

The study design was approved by the ethics committees of INCMNSZ and UCLA, and all subjects provided written informed consent.

“The study design was approved by the ethics committees of INCMNSZ and UCLA, and all subjects provided written informed consent.”