The DOI matches its Crossref record; 73 of the 73 references it cites were found in a registry or an index; none of the 55 sources its claims cite is checked for support yet.
Genome-wide detection of tandem DNA repeats that are expanded in autism
Open accessAbstract
Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic disorders1. Their involvement in disorders with complex genetics is largely unknown, as is the extent of their heterogeneity. Here we investigated the genome-wide characteristics of tandem repeats that had motifs with a length of 2–20 base pairs in 17,231 genomes of families containing individuals with autism spectrum disorder (ASD)2,3 and population control individuals4. We found extensive polymorphism in the size and sequence of motifs. Many of the tandem repeat loci that we detected correlated with cytogenetic fragile sites. At 2,588 loci, gene-associated expansions of tandem repeats that were rare among population control individuals were significantly more prevalent among individuals with ASD than their siblings without ASD, particularly in exons and near splice junctions, and in genes related to the development of the nervous system and cardiovascular system or muscle. Rare tandem repeat expansions had a prevalence of 23.3% in children with ASD compared with 20.7% in children without ASD, which suggests that tandem repeat expansions make a collective contribution to the risk of ASD of 2.6%. These rare tandem repeat expansions included previously undescribed ASD-linked expansions in DMPK and FXN, which are associated with neuromuscular conditions, and in previously unknown loci such as FGF14 and CACNB1. Rare tandem repeat expansions were associated with lower IQ and adaptive ability. Our results show that tandem DNA repeat expansions contribute strongly to the genetic aetiology and phenotypic complexity of ASD. Genome-wide analysis of tandem DNA repeats in the genomes of individuals with autism spectrum disorder and control participants reveals a strong contribution of tandem repeat expansions to the genetic aetiology and phenotypic complexity of autism spectrum disorder.
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55 Own result · 31 Not checked yet · 21 Own method · 12 Own interpretation · 2 No basis given
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“Rare tandem repeat expansions had a prevalence of 23.3% in autism-affected children versus 20.7% in unaffected children”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Abstract
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“We found extensive polymorphism in motif size and sequence.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Abstract
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“At 2,588 loci, gene-associated tandem repeat expansions that were rare among population controls were significantly more prevalent among individuals with autism than their unaffected siblings”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Abstract
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“These were associated with lower IQ and adaptive ability.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Abstract
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“particularly in exons and near splice junctions”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Abstract
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“in genes related to nervous system development and cardiovascular system or muscle”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Abstract
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“revealing that a given tract could have more than one motif, with ~1.2 different motifs per region”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Wide variability of tandem repeats
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“This resulted in 2,588 tandem repeat-containing regions (3,339 motifs) being categorized as rare tandem repeat expansions”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Rare tandem repeat expansions in ASD
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“they were prevalent in known polymorphic simple sequence repeat regions previously detected by Tandem Repeats Finder35 in 1,031,708 locations in the human reference genome (odds ratio (OR)=6.24; p<2.2×10−16)36.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Wide variability of tandem repeats
What the sources say
- Not checked yetcites [35] Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999). source
- Not checked yetcites [36] Willems, T., Gymrek, M., Highnam, G., Mittelman, D. & Erlich, Y. The landscape of human STR variation. Genome Res. 24, 1894–1904 (2014). source
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In the paper
“One of the potentially novel mapped fragile sites was FRA19B, which overlapped with a CGG tandem repeat detected at the 5’ untranslated region in LINGO3.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Wide variability of tandem repeats
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Probably not a substantial claim. 40
- It may state two separate claims as one. 21
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“Many correlated with cytogenetic fragile sites.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Abstract
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In the paper
“These tandem repeat-containing regions were more prevalent in GC-rich regions (OR=1.05; p<2.2×10−16) and all (common and rare) known fragile site regions (OR=1.12; p=1.2×10−4)”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Wide variability of tandem repeats
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In the paper
“Of the motifs, 5.6% were composed only of A or T nucleotides, and only 0.4% were composed of C or G only”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Wide variability of tandem repeats
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In the paper
“There were 2,529 regions (8%) with more than one motif, and as many as 92 different motifs in a single region”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Wide variability of tandem repeats
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“tandem repeat-containing regions we identified co-localized to 9 of 11 (81.8%) of the molecularly mapped rare folate-sensitive fragile sites37, all at CG-containing tandem repeats”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Wide variability of tandem repeats
What the sources say
- Not checked yetcites [37] Bignell, G. R. et al. Signatures of mutation and selection in the cancer genome. Nature 463, 893–898 (2010). source
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In the paper
“The number of motifs per region varied across chromosomes in an apparently non-random manner”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Wide variability of tandem repeats
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“The most common motif size was 2 bp, found in 27.7% of repeat tracts.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Wide variability of tandem repeats
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“In genic regions, tandem repeat-containing regions were more common than the genomic average in upstream (OR=1.33; p<2.2×10−16) (1 kb from transcription start sites) and 5’ untranslated (OR=1.2; p<2.2×10−16) regions but less common in exonic (OR=0.61; p<2.2×10−16) and 3’ untranslated (OR=0.43; p<2.2×10−16) regions”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Wide variability of tandem repeats
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In the paper
“the motifs were predominantly (>40%) AC- (GT- on the opposite strand) or AG- (CT- on the opposite strand) rich”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Wide variability of tandem repeats
What the sources say
- Not checked yetcites [34] Subramanian, S., Mishra, R. K. & Singh, L. Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol. 4, R13 (2003). source
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In the paper
“In the smallest size range, even-numbered motif sizes (2, 4 and 6 bp) notably outnumbered the odd-numbered sizes (3 and 5 bp), whereas no such trend was evident among the larger motifs”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Wide variability of tandem repeats
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“We also detected an enrichment for transmitted large tandem repeats in SSC unaffected siblings; however, these tandem repeats were more likely to be further expanded in ASD-affected individuals”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Functional effects of rare expansions
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In the paper
“nervous system development and cardiovascular system or muscle were also among the top enriched gene sets”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Functional effects of rare expansions
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“These rare tandem repeat expansions generally represented further expansions from already-large tandem repeats from the previous generation (but not in the unaffected siblings)”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Rare tandem repeat expansions in ASD
plaindirectn = 1,812- Asserted: passes — The authors put it forward as true.
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In the paper
“we found that in individuals with ASD, these large tandem repeats were more likely to be transmitted and were more prevalent in exons and splice sites”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Functional effects of rare expansions
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“We identified 7 individuals with ASD from unrelated families and 1 unaffected sibling that carry rare CTG repeat expansions in DMPK (experimentally validated with repeat-primed PCR and Southern blotting”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > ASD-relevant tandem repeat regions
plaincorrelationaln = 7- Asserted: passes — The authors put it forward as true.
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In the paper
“subjects with rare tandem repeat expansions had lower IQ (Wilcoxon test, p=0.001) and Vineland Adaptive Behavioral standard scores (Wilcoxon test, p=0.019)”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > ASD-relevant tandem repeat regions
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In the paper
“Rare tandem repeat expansions in 57 loci (having a higher frequency in ASD-affected individuals than unaffected siblings) within these enriched gene sets collectively accounted for 2.2% (40 of 1,812) of the ASD cases in SSC (OR=4.76; p=2×10−5), and 2.5% in the entire cohorts (129 of 5,194)”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > ASD-relevant tandem repeat regions
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In the paper
“we have revealed far more extensive variability among tandem repeat sequences than previously recognized in the human genome, with 8% of the tandem repeats interrogated having more than one motif detected.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Discussion
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“Note that the length of the premutation CTG repeats (42 CTGs) was close to the read length of the HiSeq X platform (150 bp).”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Extended Data
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In the paper
“While short CTG repeats were correctly sized by ExpansionHunter (the results were perfectly matched with fragment analysis), slight discrepancies were observed in the estimates for premutation alleles between ExpansionHunter and PCR-based fragment analysis.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Extended Data
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In the paper
“The father has only the unexpanded allele.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Extended Data
plainn = 2- Asserted: passes — The authors put it forward as true.
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In the paper
“In both families, the expansion is transmitted from the mother to the child (samples highlighted in red).”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Extended Data
plaindirectn = 2- Asserted: passes — The authors put it forward as true.
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“Of the 3 distributions, c is closest to the normal distribution.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Extended Data
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In the paper
“When expanded, they have been associated with >40 monogenic disorders1.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Abstract
What the sources say
- Not checked yetcites [1] López Castel, A., Cleary, J. D. & Pearson, C. E. Repeat instability as the basis for human diseases and as a potential target for therapy. Nat. Rev. Mol. Cell Biol. 11, 165–170 (2010). source
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In the paper
“Genetic factors contribute to the etiology of ASD; twin studies estimate heritability in the 50–90% range, and recurrence in families is ~20%8,9.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Introduction
What the sources say
- Not checked yetcites [8] Ozonoff, S. et al. Recurrence risk for autism spectrum disorders: a Baby Siblings Research Consortium study. Pediatrics 128, e488–e495 (2011). source
- Not checked yetcites [9] Risch, N. et al. Familial recurrence of autism spectrum disorder: evaluating genetic and environmental contributions. Am. J. Psychiatry 171, 1206–1213 (2014). source
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In the paper
“Our results revealed a strong contribution of tandem DNA repeat expansions to the genetic etiology and phenotypic complexity of autism.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Abstract
boosteddirectn = 17,231- Asserted: passes — The authors put it forward as true.
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In the paper
“the causal genetic variants thus far identified generally confer less risk than expected from empirical estimates of heritability6.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Introduction
What the sources say
- Not checked yetcites [6] Manolio, T. A. et al. Finding the missing heritability of complex diseases. Nature 461, 747–753 (2009). source
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In the paper
“twin studies estimate heritability in the 50–90% range”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Introduction
What the sources say
- Not checked yetcites [8] Ozonoff, S. et al. Recurrence risk for autism spectrum disorders: a Baby Siblings Research Consortium study. Pediatrics 128, e488–e495 (2011). source
- Not checked yetcites [9] Risch, N. et al. Familial recurrence of autism spectrum disorder: evaluating genetic and environmental contributions. Am. J. Psychiatry 171, 1206–1213 (2014). source
hedged- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“They included novel autism-linked tandem repeat expansions in DMPK and FXN, known for neuromuscular conditions, and in novel loci such as FGF14 and CACNB1.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Abstract
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“recurrence in families is ~20%8,9”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Introduction
What the sources say
- Not checked yetcites [8] Ozonoff, S. et al. Recurrence risk for autism spectrum disorders: a Baby Siblings Research Consortium study. Pediatrics 128, e488–e495 (2011). source
- Not checked yetcites [9] Risch, N. et al. Familial recurrence of autism spectrum disorder: evaluating genetic and environmental contributions. Am. J. Psychiatry 171, 1206–1213 (2014). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“individuals with ASD have a two- to three-fold increase in the number of rare copy number variations (CNVs) and de novo loss-of-function (nonsense, frameshift, and splice site) variants compared to their unaffected siblings11–14.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Introduction
What the sources say
- Not checked yetcites [11] De Rubeis, S. et al. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature 515, 209–215 (2014). source
- Not checked yetcites [12] Iossifov, I. et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature 515, 216–221 (2014). source
- Not checked yetcites [13] Sanders, S. J. et al. Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci. Neuron 87, 1215–1233 (2015). source
- Not checked yetcites [14] Yuen, R. K. C. et al. Genome-wide characteristics of de novo mutations in autism. NPJ Genom. Med. 1, 16027 (2016). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“more than 100 genes and loci are known to be associated with increased likelihood of ASD2,13.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Introduction
What the sources say
- Not checked yetcites [2] Yuen, R. K. C. et al. Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. Nat. Neurosci. 20, 602–611 (2017). source
- Not checked yetcites [13] Sanders, S. J. et al. Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci. Neuron 87, 1215–1233 (2015). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“the unstable CGG tract of FMR1 has been linked to intellectual delay in fragile X syndrome, fragile X premature ovarian insufficiency, fragile X associated ataxia, endocrine, autoimmune, metabolic disease, and ASD29.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Introduction
What the sources say
- Not checked yetcites [29] Hagerman, R. J. et al. Fragile X-associated neuropsychiatric disorders (FXAND). Front. Psychiatry 9, 564 (2018). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“We used sex and number of intergenic tandem repeat expansions as covariates in the statistical tests”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Rare tandem repeat expansions in ASD
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“Approximately 5% of individuals with DM1 also have ASD45,46.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > ASD-relevant tandem repeat regions
What the sources say
- Not checked yetcites [45] Shoubridge, C. et al. Is there a Mendelian transmission ratio distortion of the c.429_452dup(24bp) polyalanine tract ARX mutation? Eur. J. Hum. Genet. 20, 1311–1314 (2012). source
- Not checked yetcites [46] Ekström, A.-B., Hakenäs-Plate, L., Samuelsson, L., Tulinius, M. & Wentz, E. Autism spectrum conditions in myotonic dystrophy type 1: a study on 57 individuals with congenital and childhood forms. Am. J. Med. Genet. B. Neuropsychiatr. Genet. 147B, 918–926 (2008). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Preferential transmission of premutated or expanded repeats to unaffected, subclinical, and affected individuals has been observed in many different repeat-related diseases42–44.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > Functional effects of rare expansions
What the sources say
- Not checked yetcites [42] Trost, B. et al. A comprehensive workflow for read depth-based identification of copy-number variation from whole-genome sequence data. Am. J. Hum. Genet. 102, 142–155 (2018). source
- Not checked yetcites [43] Takiyama, Y. et al. Single sperm analysis of the CAG repeats in the gene for Machado–Joseph disease (MJD1): evidence for non-Mendelian transmission of the MJD1 gene and for the effect of the intragenic CGG/GGG polymorphism on the intergenerational instability. Hum. Mol. Genet. 6, 1063–1068 (1997). source
- Not checked yetcites [44] Dean, N. L. et al. Transmission ratio distortion in the myotonic dystrophy locus in human preimplantation embryos. Eur. J. Hum. Genet. 14, 299–306 (2006). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“whose expansion to greater than 50 repeat units causes myotonic dystrophy type 1 (DM1) (OMIM ID: 160900)”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Results > ASD-relevant tandem repeat regions
What the sources say
- Not checked yetcites OMIM ID: 160900
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our strategy of genome-wide detection of expanded tandem repeats in ASD also provides a model to search for missing heritability in other complex disorders.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Discussion
plain- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“the method we developed here only provides an estimated relative aggregated length of the tandem repeat tracts and does not resolve zygosity or orientation.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Discussion
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“For tandem repeats that were detected with multiple different motifs at the same repeat-containing regions (e.g., CACNB1 and FXN) (Extended Data Fig. 9), we performed Sanger sequencing on the PCR-amplified alleles after gel extraction to confirm the presence of the reported motifs.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Methods > Validation of tandem repeat expansions
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“This value was selected because it resulted in both a reasonable number of outliers and good agreement between outliers detected from EHdn and outliers detected in corresponding loci from ExpansionHunter”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Methods > Detection of tandem repeat expansions
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“there are tandem repeat-associated diseases for which one or two additional repeat units leads to disease. Such changes will be missed by EHdn.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Methods > Detection of tandem repeat expansions
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“No individual had an extreme number of rare tandem repeat expansions (Supplementary Fig. 4).”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Methods > Detection of tandem repeat expansions
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“As a result, samples that did not meet this size minimum for a given region were left without EHdn’s size estimation.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Methods > Detection of tandem repeat expansions
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Rests on an assumption: For EHdn to detect a tandem repeat, the repeat must be longer than the sequence read length (e.g., >150 bp).
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Results from PCR and gel electrophoresis were consistently reproduced at least twice for CACNB1 and FXN loci (see Supplementary Figures).”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Extended Data
plainn = 2- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Repeat-primed PCR experiments were consistently reproduced at least three times for the large expansions.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Informed consent was obtained from all participants through the recruitment sites.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Methods > Samples
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“We estimated family-wise error rate (FWER) to adjust for multiple comparisons.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Methods > Burden analysis
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“We avoided sex bias by performing the test only on autosomal regions, as well as using sex as a covariate for correction of the regression model.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Methods > Burden analysis
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“We further accounted for the bias in number of rare tandem repeat expansions per subject in genic, functional, and gene set burden tests by covarying the number of rare tandem repeat expansions found in intergenic regions.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Methods > Burden analysis
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“For samples that appeared to be homozygous for the tandem repeat length, we validated the presence of expanded tandem repeats by repeat-primed PCR (RP-PCR) and/or Southern blot.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Methods > Validation of tandem repeat expansions
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Repeat sizing experiments of PCR-amplifiable samples were consistently reproduced at least twice.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Samples included were mutually exclusive to each other and there were no replicates (randomization not applicable).”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Methods > Statistical comparisons of means
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The study protocol was approved by The Hospital for Sick Children’s Research Ethics Board (REB).”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Methods > Samples
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The validation of the tandem repeat length estimated by ExpansionHunter or EHdn was done by fragment analysis with FAM-labelled primers and capillary electrophoresis.”
§ Genome-wide detection of tandem DNA repeats expanded in autism > Methods > Validation of tandem repeat expansions
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
The paper relies on this without support.
The involvement of tandem DNA repeats in complex disorders and the extent of their heterogeneity are largely unknown.
“Their involvement in complex disorders is largely unknown, as is the extent of their heterogeneity.”
The paper relies on this without support.
The population control cohorts used are representative of the general population for estimating the rarity of tandem repeat expansions.
“we used 1,612 genomic samples from GTEx32 and the Mayo Clinic33”
The paper relies on this without support.
For EHdn to detect a tandem repeat, the repeat must be longer than the sequence read length (e.g., >150 bp).
“For a tandem repeat to be detected by EHdn, it must be larger than the sequence read length (e.g., > 150 bp).”
The paper relies on this without support.
DBSCAN may fail to detect outliers when only a few samples have genotype data.
“Similarly, DBSCAN might fail to detect outliers when only a few samples have genotype data.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“yet emerging evidence suggests a role for other classes (for example, rare inherited and de novo tandem repeats) of genetic variants as well17,19,60,61.”
From Genetic correlates of phenotypic heterogeneity in autism (2022) · cites this paper as [60]
Experimental — accuracy not yet measured
Citations
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Self-citationThe molecular pathogenesis of repeat expansion diseases
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Short tandem repeats bind transcription factors to tune eukaryotic gene expressionPreprint
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The Importance of Large-Scale Genomic Studies to Unravel Genetic Risk Factors for Autism
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Modification of Huntington’s disease by short tandem repeats
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Self-citationThe rate and spectrum of new mutations in mice inferred by long-read sequencingPreprint
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Whole-genome sequencing identifies novel genes for autism in Chinese trios
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Metadata
- Authors
- Trost, B., Engchuan, W., Nguyen, C. M., Thiruvahindrapuram, B., Dolzhenko, E., Backstrom, I., Mirceta, M., Mojarad, B. A., Yin, Y., Dov, A., Chandrakumar, I., Prasolava, T., Shum, N., Hamdan, O., Pellecchia, G., Howe, J. L., Whitney, J., Klee, E. W., Baheti, S., Amaral, D. G., Anagnostou, E., Elsabbagh, M., Fernandez, B. A., Hoang, N., Lewis, M. E. S., Liu, X., Sjaarda, C., Smith, I. M., Szatmari, P., Zwaigenbaum, L., Glazer, D., Hartley, D., Stewart, A. K., Eberle, M. A., Sato, N., Pearson, C. E., Scherer, S. W., & Yuen, R. K. C.
- Affiliations
- Hospital for Sick Children (CA)
- University of Toronto (CA)
- Illumina (United States) (US)
- Mayo Clinic (US)
- University of California Davis Medical Center (US)
- Centre Azrieli de recherche sur l'autisme (CA)
- Memorial University of Newfoundland (CA)
- University of British Columbia (CA)
- Queen's University (CA)
- Dalhousie University (CA)
- University of Alberta (CA)
- Verily Life Sciences LLC (United States) (US)
- Autism Speaks (US)
- Corresponding author
- Yuen, Ryan K. C.
- ORCID
- Trost, Brett
- Engchuan, Worrawat
- Thiruvahindrapuram, Bhooma
- Dolzhenko, Egor
- Backstrom, Ian
- Mojarad, Bahareh A.
- Yin, Yue
- Pellecchia, Giovanna
- Klee, Eric W.
- Baheti, Saurabh
- Amaral, David G.
- Anagnostou, Evdokia
- Elsabbagh, Mayada
- Fernandez, Bridget A.
- Hoang, Ny
- Lewis, M. E. Suzanne
- Liu, Xudong
- Sjaarda, Calvin
- Smith, Isabel M.
- Zwaigenbaum, Lonnie
- Glazer, David
- Hartley, Dean
- Stewart, A. Keith
- Eberle, Michael A.
- Sato, Nozomu
- Pearson, Christopher E.
- Scherer, Stephen W.
- Yuen, Ryan K. C.
- Venue
- Nature
- Published
- 2020-07-27
- Volume
- 586
- Issue
- 7827
- Pages
- 80-86
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC9348607
- OpenAlex
- W3044594590
- Semantic Scholar
- 24871e7070485b8f5dc5da18e1a1f12aa9f1a514
- Cited by
- 238
- References
- 73
- Citations by year
- 2026: 24 · 2025: 36 · 2024: 39 · 2023: 36 · 2022: 47 · 2021: 44 · 2020: 10
- FWCI
- 20.05
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institute of Mental Health (R01MH103371)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- tandem repeat expansion, autism spectrum disorder, genetic aetiology, fragile sites, DMPK, frataxin, FGF14, neuromuscular disorders, intellectual disability, phenotypic complexity, splice junctions
- MeSH terms
- Autism Spectrum Disorder, Frataxin, Female, Fibroblast Growth Factors, Humans, Intelligence, Male, Polymorphism, Genetic, Genome, Human, Genetic Predisposition to Disease, Tandem Repeat Sequences, Genomics, Iron-Binding Proteins, DNA Repeat Expansion, Nucleotide Motifs, Myotonin-Protein Kinase
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