Excess of rare, inherited truncating mutations in autism

May combine two claims.

In genes with RVIS below the 10th percentile, 50.6% of probands (903/1,786) and 47.9% of siblings (855/1,786) inherited LGD SNVs, a 2.7% difference.

“we found that 50.6% of probands (903/1,786 quads) and 47.9% of siblings (855/1,786 quads) contained such events, respectively, a difference of 2.7%.”

• AssumptionThe authors state this as an assumption: Protein-truncating mutations in genes intolerant to deleterious variation are more likely to be pathogenic.

May combine two claims.

Probands with full-scale IQ 70-100 had an odds ratio of 1.18 (p=0.002), while those with IQ above 100 had a lower non-significant odds ratio of 1.06.

“we found that probands with full-scale IQ between 70–100 had an odds ratio of 1.18 (p = 0.002), whereas those with an IQ above 100 had a lower, non-significant odds ratio of 1.06”

• AssumptionThe authors state this as an assumption: Protein-truncating mutations in genes intolerant to deleterious variation are more likely to be pathogenic.

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

In SSC probands, IQ and clinical diagnosis are weakly correlated (r2=0.18, p<1×10−10).

“For probands in the SSC, IQ and clinical diagnosis are weakly correlated (Supplementary Figure 3; r2 = 0.18, p < 1×10−10)”

May combine two claims.

For 1,575 probands diagnosed with autism or PDD, inherited gene-disruptive mutation odds ratios were 1.15 and 1.18 (p=0.001 and 0.05).

“For the 1,575 probands with a diagnosis of “autism” or “pervasive developmental disorder” (PDD), the odds ratio was 1.15 and 1.18 (p = 0.001 and 0.05), respectively.”

• AssumptionThe authors state this as an assumption: Protein-truncating mutations in genes intolerant to deleterious variation are more likely to be pathogenic.

May combine two claims.

Gene-level RV-TDT produced several promising candidate genes, but none survived multiple-testing correction.

“Several promising candidate genes emerged (Supplementary Table 3) although none survived a multiple-testing correction (Online Methods).”

May combine two claims.

For genes in the lowest 1% of RVIS, the proband-sibling burden odds ratio reaches 1.4, but this comparison is not statistically significant because few mutations are present.

“At the extreme, the burden between probands and siblings in genes with the lowest 1% of all RVIS values reaches an odds ratio of 1.4 (although this comparison is not statistically significant due to the small number of mutations present at this threshold in the current dataset).”

• AssumptionThe authors state this as an assumption: Protein-truncating mutations in genes intolerant to deleterious variation are more likely to be pathogenic.

The quote only partly states this claim.

Small maternally inherited CNVs are enriched for CHD8 target genes (p=7.4×10−3).

“that are enriched in CHD8 target genes (p=7.4×10−3)”

• Also stated in: § CNV discovery and validation · plain

  “this enrichment was strongest for small duplications (<100 kbp) (OR = 1.5, p = 0.05, Fisher’s exact test, p = 7.4×10−3, paired t-test).”

May combine two claims.

For SRS-discordant quads, the proband-sibling differential for private LGD SNVs in conserved genes (RVIS<10) was 3.7%, compared with 1.6% in SRS-concordant quads.

“we observed a stronger proband-sibling differential of 3.7% for private LGD SNVs in conserved genes (RVIS < 10) for SRS discordant quads only (484 probands with events of 923 discordant quads, siblings 450/923), while SRS concordant quads had only a 1.6% differential (probands 419/863 and siblings 405/863).”

• AssumptionThe authors state this as an assumption: Protein-truncating mutations in genes intolerant to deleterious variation are more likely to be pathogenic.

May combine two claims.

Attributable fractions were 6.62% [4.18,8.99] for de novo LGD SNVs, 8.54% [−24.23,32.66] for private inherited LGD SNVs, 2.92% [1.37,4.44] for de novo CNVs, and 3.18% [−3.71,9.6] for rare inherited CNVs.

“de novo LGD SNVs (6.62% [4.18%, 8.99%]), private, inherited LGD SNVs (8.54% [−24.23%, 32.66%]), de novo CNVs (2.92% [1.37%, 4.44%]), and rare, inherited CNVs (3.18% [−3.71%, 9.6%]).”

May combine two claims.

The analysis found a paternally inherited two-exon intragenic deletion of NRXN3 and a de novo missense mutation of NLGN2 in proband 13367.p1.

“our analysis uncovered a paternally inherited two-exon intragenic deletion of NRXN3 and a de novo missense mutation of NLGN2 in proband 13367.p1”

The quote only partly states this claim.

The CHD8 target enrichment was strongest for small duplications (<100 kbp) (OR=1.5, p=0.05 Fisher; p=7.4×10−3 paired t-test).

“In particular, this enrichment was strongest for small duplications (<100 kbp) (OR = 1.5, p = 0.05, Fisher’s exact test, p = 7.4×10−3, paired t-test).”

May combine two claims.

For LGD SNVs, maternally private inherited LGD SNVs with RVIS<50 had the highest attributable fraction in male proband families (8.32% [0.56,15.48]), while female proband families had −2.33% [−29.06,18.87].

“For the LGD SNVs, we were able to identify the maternally private, inherited LGD SNVs with RVIS < 50 as the category with the highest attributable fraction (estimated) in the population (8.32% [0.56%, 15.48%]) in the male proband families whereas the female proband families had a value of −2.33% [−29.06%, 18.87%] in this same category.”

• AssumptionThe authors state this as an assumption: Protein-truncating mutations in genes intolerant to deleterious variation are more likely to be pathogenic.

May combine two claims.

Inherited CNVs showed no overall enrichment for FMRP (p=0.22) or CHD8 (p=0.19) targets.

“Although no overall enrichment of FMRP (p = 0.22) or CHD8 (p = 0.19) targets was observed among inherited CNVs”

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

Using two SNV callers identified 77 additional de novo SNVs that previous studies missed.

“the application of two SNV callers identified 77 additional de novo SNVs previously missed 9.”

• cites [9] Iossifov, I. et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature 515, 216–221 (2014). sourceNot checked yet

  Not checked in the free run.

May combine two claims.

Each de novo CNV raised ASD risk 2.05-fold, and each de novo SNV raised risk 1.72-fold (p=0.0004 and p<1×10−7).

“each de novo CNV increased the risk for ASD by 2.05-fold, while each de novo SNV increased risk by 1.72-fold (p = 0.0004 and p < 1 ×10−7, respectively).”

May combine two claims.

De novo CNVs were enriched for both FMRP and CHD8 targets (OR=3.1, p=6.6×10−4 and OR=2.7, p=1.7×10−3, Fisher; p=1.4×10−4 and p=2.6×10−4, paired t-test).

“Both FMRP and CHD8 targets were enriched in de novo CNVs (OR = 3.1, p = 6.6×10−4 and OR = 2.7, p = 1.7×10−3, Fisher’s exact test and p=1.4×10−4 and p=2.6×10−4, paired t-test, respectively)”

May combine two claims.

De novo CNVs show a 2.4-fold excess in probands (n=79) versus siblings (n=33) (p=6.7×10−5), driven mainly by deletions (p=4.2×10−5) and not duplications (p=0.18).

“Restricting the analysis to de novo CNVs, we identified, as expected, a more significant 2.4-fold excess (p = 6.7×10−5, paired t-test) in probands (n = 79) when compared to siblings (n = 33) driven primarily by deletions (p = 4.2×10−5, paired t-test) and not duplications (p = 0.18, paired t-test)”

May combine two claims.

Maternally inherited autosomal deletions containing CHD8 targets showed modest macrocephaly enrichment (OR=2.9, p=0.03 Fisher), including smaller deletions (<100 kbp, OR=3.5, p=0.04).

“we observed a modest enrichment for macrocephaly in maternally inherited autosomal deletions containing CHD8 targets (OR = 2.9, p = 0.03, Fisher’s exact test), including smaller deletions (<100 kbp, OR = 3.5, p = 0.04, Fisher’s exact test).”

May combine two claims.

RIMS1 showed nominally significant transmission disequilibrium of private disruptive events to probands (p=0.013) but not siblings (p=0.841).

“we also find a nominally significant transmission disequilibrium of private, disruptive events of RIMS1 to probands (p = 0.013, TDT-Combined Multivariate and Collapsing (CMC) analytical 22) but not siblings (p = 0.841)”

• cites [22] Constantino, J.N. et al. Validation of a brief quantitative measure of autistic traits: comparison of the social responsiveness scale with the autism diagnostic interview-revised. J. Autism Dev. Disord. 33, 427–433 (2003). sourceNot checked yet

  Not checked in the free run.

May combine two claims.

Stratifying private inherited LGD SNVs by inheritance and RVIS showed a clear maternal contribution (7.15% [−0.25,14.01]) and no paternal contribution (1.01% [−6.56,8.04]).

“the results become much tighter and show a clear contribution for maternal events (7.15% [−0.25%, 14.01%]) and not for the paternal events (1.01% [−6.56%, 8.04%]).”

• AssumptionThe authors state this as an assumption: Protein-truncating mutations in genes intolerant to deleterious variation are more likely to be pathogenic.

May combine two claims.

De novo CNVs in probands were larger than those in siblings (p=0.03) and affected genes with lower total RVIS values (p=0.02).

“Overall, de novo CNVs were larger in probands than in siblings (p = 0.03, Wilcoxon) and carried genes with significantly lower total RVIS values (p = 0.02, Wilcoxon).”

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

An additional 132 previously called but unconfirmed events were validated by Sanger sequencing, bringing the total to 209 validated de novo SNVs and indels.

“In addition, we also validated by Sanger sequencing another 132 previously called 9 but not confirmed events, resulting in a total of 209 validated de novo SNVs and indels (Supplementary Table 2).”

• cites [9] Iossifov, I. et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature 515, 216–221 (2014). sourceNot checked yet

  Not checked in the free run.

May combine two claims.

The three highest ranked genes-RIMS1, CUL7, and CSMD1-each show brain-specific patterns or known neural functions.

“the three highest ranked genes—RIMS1, CUL7 and CSMD1—each display brain-specific patterns or have identified neural functions”

May combine two claims.

CSMD1 has three de novo missense mutations in probands, four LGD SNVs (one shared with a sibling and one in a trio), and five rare inherited CNVs (one shared with a sibling and one in a trio).

“CSMD1 has three de novo missense mutations in probands, four LGD SNVs (one is shared with a sibling and one is found in a trio), and five rare, inherited CNVs (where one is shared with a sibling and one is found in a trio).”

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

Among the 77 validated novel de novo SNVs, there were 51 missense, 11 frameshift, 6 stop-gained, 4 splice-site donor, 3 splice-site acceptor, 1 stop-lost, and 1 codon change plus codon deletion.

“These SNVs included various functional classes: 1 codon change plus codon deletion, 11 frameshift, 51 missense, 3 splice-site acceptor, 4 splice-site donor, 6 stop-gained, and 1 stop-lost.”

May combine two claims.

Validated mutations established recurrent de novo mutations for GIGYF2 and SSPO and added a new LGD mutation to GIGYF1 and ASH1L, for three LGD de novo mutations each.

“Notably, these validated mutations established recurrent de novo mutations for GIGYF2 and SSPO (a brain-secreted protein involved in axon growth) as well as added a new LGD mutation to GIGYF1 and ASH1L for a total of three LGD de novo mutations each.”

May combine two claims.

CUL7 has two de novo and two LGD-inherited mutations in probands and none in siblings.

“CUL7 has two de novo and two LGD-inherited mutations in probands (none in siblings)”

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

The reanalysis pipeline predicted 1,544 de novo SNVs not previously reported.

“Our reanalysis pipeline predicted 1,544 de novo SNVs not previously reported (Supplementary Table 1).”

May combine two claims.

Post hoc classifiers suggested proband allele balance was the best individual predictor of de novo variant validation and that classification models could accurately predict which events would validate.

“Post hoc analysis using three different classifiers (support vector machine (SVM), decision tree and random forest) suggested that the proband’s allele balance was the best individual predictor of de novo variant validation and that classification models could accurately predict which events would be most likely to validate”

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

Sanger sequencing validated 77 of 141 tested novel candidate de novo SNVs (55%).

“Using Sanger sequencing, we attempted validation of 141 (of the 1,544) previously unidentified de novo variants, including all novel LGD (stop-gain, frameshift and splice-site) events as well as recurrent missense mutations in autism candidate genes 55. We were able to validate 77 new sites (55%).”

• cites [55] Scharpf, R.B., Irizarry, R.A., Ritchie, M.E., Carvalho, B. & Ruczinski, I. Using the R package crlmm for genotyping and copy number estimation. J. Stat. Softw. 40, 1–32 (2011). sourceNot checked yet

  Not checked in the free run.

May combine two claims.

Of 141 selected for Sanger validation, 55% (77) confirmed as de novo, plus 132 additional events previously called but not confirmed.

“Of these new sites, 55% (77) confirmed as de novo as well as an additional 132 events that had been called but not confirmed in previous studies”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims. The quote only partly states this claim.

Array CGH testing of 50 additional de novo CNVs in individuals without SNP microarray data validated 26 events: 21 were de novo and 5 were transmitted.

“Of these CNV events, 26 CNVs were validated, of which 21 were confirmed to be de novo while 5 CNVs were transmitted events (Supplementary Table 5).”

• cites [12] Krumm, N. et al. Transmission disequilibrium of small CNVs in simplex autism. Am. J. Hum. Genet. 93, 595–606 (2013). sourceNot checked yet

  Not checked in the free run.

May combine two claims.

When a squared term for total mutation count was added to the logistic regression, the linear term stayed significant (OR = 1.20, p = 0.002), whereas the squared term did not (OR = 1.00, p = 0.59).

“In this model, the simple sum was again significant (OR = 1.20, p = 0.002), but the squared sum term was not (OR = 1.00, p = 0.59).”

May combine two claims.

The four modeled mutation classes contribute additively and independently to ASD risk.

“These results suggest that each of the four types of mutations modeled additively contribute to the risk of ASD and that they do so in a statistically independent manner.”

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

The intersection variant set had median Ti/Tv ratios of 2.94 for all sites, 2.95 for dbSNP sites, and 1.94 for novel sites.

“The intersection set of variants had a median Ti/Tv ratio of 2.94 (95% CI 2.79–3.03) for all sites, 2.95 (95% CI 2.83–3.04) for dbSNP sites, and 1.94 (95% CI 1.05–2.75) for novel sites.”

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

In 3,052 offspring from 1,796 families, a median of 17,731 overlapping SNPs were compared, yielding a median genotype-level concordance of 99.4% between exome SNP calls and Illumina SNP microarray data.

“we compared SNPs from exome calls with SNP calls from existing Illumina SNP microarray data 19 (Sanders personal communication) and found the median genotype-level concordance to be 99.4% (for a median of 17,731 overlapping SNPs in 3,052 offspring in 1,796 families for which microarray data was available).”

• cites [19] Petrovski, S., Wang, Q., Heinzen, E.L., Allen, A.S. & Goldstein, D.B. Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet. 9, e1003709 (2013). sourceNot checked yet

  Not checked in the free run.

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

The number of rare variant alleles in probands and siblings was highly correlated (r2=0.99).

“As expected, the number of rare variant alleles in probands and siblings were highly correlated (Figure 1a, r2 = 0.99)”

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

For inherited mutations in the intersection set, 98.6% of sites were present in dbSNP, and 99.7% of those matched the alternate allele.

“Of all inherited mutations in the intersection set, an average of 341 (95% CI 133–632) sites were novel and not observed in dbSNP (v137); 98.6% of sites were in dbSNP with a concordance rate of 99.7%”

May combine two claims.

Extrapolating proband allele balance across 771 untested candidate variants suggests 463 (60%) additional true de novo variants at an allele balance cutoff >0.3; random forest predicts 445 (58%) additional de novo variants would validate.

“Extrapolating the proband’s allele balance across all untested candidate variants in probands (n = 771) suggests that there are 463 (60%) additional true de novo variants in probands (at an allele balance cutoff > 0.3); similarly, the predictions generated by the random forest model suggest 445 (58%) additional de novo variants in probands would validate.”

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

A median of 98.6% of sites were in dbSNP, and 99.7% of those agreed on the alternate allele.

“conversely, a median of 98.6% of sites were in dbSNP and 99.7% of those were in agreement with respect to the alternate allele.”

Classified as probably not a substantial claim.

The conditional logistic regression model included a family-level stratum to account for familial stratification.

“Additionally, we accounted for familial stratification effects by adding a family-level stratum to the model.”

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

Transmitted variants were called by both GATK HaplotypeCaller and FreeBayes and passed quality filters.

“Combined, we identified a total of 1,303,385 transmitted variants called by both GATK HaplotypeCaller and FreeBayes and passing our quality filters”

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

Fourteen families were excluded from analysis because of sample identity issues.

“We excluded 14 families for sample identity issues and concordance by center is shown in Supplementary Table 10.”

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

For the intersection set, the median Ti/Tv ratio was 2.94 (95% CI 2.79-3.03) across all sites, 2.95 (95% CI 2.83-3.04) for dbSNP sites, and 1.94 (95% CI 1.05-2.75) for novel sites.

“The intersection set of variants had a median Ti/Tv ratio of 2.94 (95% CI 2.79–3.03) for all sites, 2.95 (95% CI 2.83–3.04) for dbSNP sites, and 1.94 (95% CI 1.05–2.75) for novel sites.”

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

No significant difference in heterozygosity was observed between probands and siblings.

“with no significant difference in heterozygosity being observed between proband and sibling”

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

Among all transmitted variants, 81% were detected by both FreeBayes and GATK, 12% only by FreeBayes, and 7% only by GATK.

“Overall, 81% of all transmitted variants were found by both FreeBayes and GATK, 12% by FreeBayes alone, and 7% by GATK.”

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

For transmitted variants, a median of 98.6% of sites were present in dbSNP, and 99.7% of those matched the alternate allele.

“A median of 377 (95% CI 154–692) sites per family were novel and not observed in dbSNP (v137); conversely, a median of 98.6% of sites were in dbSNP and 99.7% of those were in agreement with respect to the alternate allele.”