Carrier Testing for Severe Childhood Recessive Diseases by Next-Generation Sequencing

In the paper

“However, concomitant analysis of normalized coverage in batches of samples appears to circumvent the need for adjustment for GC content (32), allowing more accurate detection of segmental losses.”

What the sources say

• Disputed

  The Results state that each sample received its own GC-dependent weighting before its coverage was divided by an average across samples. The Methods likewise describe normalizing a GC-corrected distribution by a multi-sample baseline. Thus, the paper does not present batch normalization as circumventing GC adjustment; it uses both steps. (LLM, conf=0.88)

  Checked by a reasoning model — may be wrong.

  cites [32] sourceExperimental — accuracy not yet measured

In the paper

“In genome research, an average depth of sequence coverage of 30-fold has been accepted as sufficient for single-nucleotide polymorphism (SNP) and nucleotide insertion or deletion (indel) detection (15–22).”

What the sources say

• Partly supported

  The Results (Accuracy of SNP detection; page not provided) say SNP-detection sensitivity is mainly limited by sequence coverage. The paper does not identify 30-fold average coverage as a sufficient threshold, and the Methods (Computational methods; page not provided) state that insertions and deletions were not considered. (LLM, conf=0.84)

  cites [15] sourceExperimental — accuracy not yet measured
• Partly supported

  The Results and Discussion section on coverage uniformity reports that 25-fold average coverage gave at least five reads for about 90% of targeted bases, and the paper evaluates SNP calls. It does not state that 30-fold coverage is an accepted sufficiency threshold or establish that depth for indel detection. (LLM, conf=0.83)

  cites [16] sourceExperimental — accuracy not yet measured
• Partly supported

  The paper reports SNP and indel detection in exomes with average coverage of 51× (Abstract; page unavailable). Its Methods specify at least 8× coverage for variant calling, but our copy does not say that an average depth of 30× is an accepted sufficient threshold for detecting both SNPs and indels. (LLM, conf=0.84)

  cites [17] sourceExperimental — accuracy not yet measured
• Partly supported

  The Conclusion (page unavailable) says average coverage of at least 20× appears the safest strategy, supporting the general point that substantial coverage aids variant detection. The paper does not identify 30× as an accepted threshold or establish its sufficiency for both SNP and indel detection; its quantified detection results concern SNPs. (LLM, conf=0.82)

  cites [18] sourceExperimental — accuracy not yet measured
• ?Could not verify

  The Methods (Read mapping and variant analysis; page unavailable) use a ≥8× coverage cutoff for sequence calls and describe coding-indel identification, but do not assess whether 30-fold average coverage is sufficient. The Discussion (page unavailable) notes that low coverage can cause missed variant calls; searches for 30-fold coverage and its sufficiency found no statement of the claimed standard. (LLM, conf=0.76)

  cites [19] sourceExperimental — accuracy not yet measured
• Partly supported

  Table 1 reports 27.83-fold coverage for the Korean genome, and the Methods Summary says SNPs and indels were identified. That supports detection at approximately 30-fold coverage in this study, but the paper does not establish that 30-fold is an accepted general threshold for sufficient detection; the main text also reports indel-detection sensitivity below 80%. (LLM, conf=0.83)

  cites [20] sourceExperimental — accuracy not yet measured
• ?Could not verify

  The Online Methods section on SNP detection describes read-count and quality filters, while the RRBS alignment section describes indel mapping; neither says that an average coverage depth of 30-fold is sufficient for detecting both. Searches for 30-fold coverage and a sufficiency threshold found no passage establishing that claim in our copy. (LLM, conf=0.74)

  cites [21] sourceExperimental — accuracy not yet measured
• Partly supported

  The passage describing the family's sequencing (section labelled Abstract; page unavailable) reports an average coverage of 40× and identification of single-nucleotide variants. It does not establish that 30× coverage is accepted as sufficient for detecting SNPs and indels, or report indel detection. (LLM, conf=0.83)

  cites [22] sourceExperimental — accuracy not yet measured

In the paper

“Criteria included test accuracy and cost, disease severity, highly penetrant recessive inheritance, and whether an intervention was available for those identified.”

What the sources say

• Partly supported

  In “The screening test: availability and characteristics” (page unavailable), the report includes test sensitivity, specificity, and cost among its criteria. “Clinical characteristics of the condition” addresses disease burden, and “Diagnosis, follow-up, treatment, and management” addresses treatment availability. The cited criteria do not establish highly penetrant recessive inheritance as a requirement. (LLM, conf=0.88)

  cites [14] sourceExperimental — accuracy not yet measured

In the paper

“To be well suited for array-based screening, however, most carriers must be accounted for by a few mutations, and most disease mutations must be nucleotide substitutions (8, 27, 28).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [8]
• ?Could not verify

  The Correspondence and Advanced search tools sections describe mutation types in HGMD, but neither discusses when array-based carrier screening is well suited. Searches for array screening and carrier frequency found no passage saying that a few mutations must account for most carriers or that most disease mutations must be nucleotide substitutions. (LLM, conf=0.72)

  cites [27] sourceExperimental — accuracy not yet measured
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [28]

In the paper

“Target capture and next-generation sequencing (NGS) have shown efficacy and, recently, scalability for resequencing human genomes and exomes, providing an alternative potential paradigm for comprehensive carrier testing (15–22).”

What the sources say

• Partly supported

  The Results (Capturing and sequencing exon targets; Reproducibility, pages unavailable) demonstrate capture and next-generation sequencing of more than 15,000 human coding exons, with high-confidence genotypes across most of the targeted space. The introductory text reports that whole human genomes had been sequenced with next-generation instruments. The paper does not demonstrate target capture at whole-exome or whole-genome scale, so the scalability claim is supported for large targeted subsets rather than those complete targets. (LLM, conf=0.84)

  cites [15] sourceExperimental — accuracy not yet measured
• Partly supported

  The Abstract and scale-up Results report effective next-generation sequencing after targeted enrichment of human genomic regions, scaled to 1.49 Mb. The Discussion describes larger-scale exon capture reported by other studies. This paper does not demonstrate scalable capture and resequencing of whole human genomes or exomes; its own experiments cover subsets of them. (LLM, conf=0.87)

  cites [16] sourceExperimental — accuracy not yet measured
• Partly supported

  The paper’s Abstract reports targeted capture and massively parallel sequencing of 12 human exomes, with sensitive variant detection across more than 300 Mb of coding sequence. Its discussion describes the approach as reproducible and able to extend a given amount of sequencing across more samples, supporting efficacy and scalability for exomes. It does not demonstrate resequencing whole human genomes. (LLM, conf=0.84)

  cites [17] sourceExperimental — accuracy not yet measured
• Partly supported

  The Abstract and Conclusion report effective target capture and NGS for sequencing exomes from eight people. They do not demonstrate scalability to large cohorts or whole-genome resequencing; the Introduction says full-genome sequencing of many people remains prohibitively costly. Page numbers are unavailable in our copy. (LLM, conf=0.86)

  cites [18] sourceExperimental — accuracy not yet measured
• Supported

  The Methods section (page unavailable) describes targeted capture and next-generation sequencing of four human exomes. The paper’s introductory discussion (page unavailable) also describes whole-genome resequencing as increasingly practical and exome resequencing as a substantially less sequencing-intensive, high-throughput alternative, supporting the broad efficacy and scalability claim. The carrier-testing application is the citing authors’ proposed use, not a finding attributed to this paper. (LLM, conf=0.85)

  cites [19] sourceExperimental — accuracy not yet measured
• Partly supported

  The main text reports massively parallel sequencing of one human genome and high-depth sequencing of selected regions using BAC clones; the Methods Summary gives a six-week run time using three instruments. This supports the feasibility of next-generation whole-genome sequencing, but the paper does not demonstrate exome resequencing, target capture, or scalability across multiple genomes. (LLM, conf=0.85)

  cites [20] sourceExperimental — accuracy not yet measured
• Partly supported

  The Main section reports high-coverage, near-complete whole-genome sequencing of two human twins, supporting the efficacy of next-generation sequencing for human genomes. The paper does not establish target capture or exome resequencing, or demonstrate scalability beyond the genomes studied (searched: target capture, exome, scalability). (LLM, conf=0.84)

  cites [21] sourceExperimental — accuracy not yet measured
• Partly supported

  The paper’s sequencing-method and family-analysis passages (section labeled Abstract; page unavailable) describe short-read sequencing of four complete human genomes and its effectiveness in narrowing candidate genes for two disorders. They do not demonstrate target capture, exome resequencing, or scalability beyond this family quartet. (LLM, conf=0.86)

  cites [22] sourceExperimental — accuracy not yet measured

In the paper

“Hitherto, important criteria precluding extension of preconception screening to most severe recessive mutations or the general population have been cost [defined in that report as an overall analytical cost requirement of <$1 per test per condition (14)] and the absence of accurate, sensitive, scalable technologies.”

What the sources say

• Partly supported

  In “The screening test: availability and characteristics” (page unavailable), the report values low-cost, high-throughput testing and sets a criterion of less than $1 per infant screened. It does not state an overall analytical cost requirement of less than $1 per test per condition; its criteria concern newborn screening, not preconception screening. (LLM, conf=0.87)

  cites [14] sourceExperimental — accuracy not yet measured

In the paper

“Given the need for highly accurate carrier detection, we required >10 uniquely aligned reads of quality score >20 and >14% of reads to call a variant (20, 21).”

What the sources say

• Partly supported

  The Methods Summary (page not available) says sequences and runs were used if their average Q scores were at least 20, and that SNPs and indels were identified using optimized filters. It does not specify more than 10 uniquely aligned reads or more than 14% variant-supporting reads; its average-quality criterion is also not the claimed per-read threshold. (LLM, conf=0.82)

  cites [20] sourceExperimental — accuracy not yet measured
• Partly supported

  The Methods Summary (page unavailable) reports 11–44× coverage and Q ≥ 20 for genotyping, while the Online Methods describe filters based on uniquely aligning reads and the percentage of reads calling a SNP. Our copy does not establish the claimed combined rule of >10 uniquely aligned reads, quality score >20, and >14% variant-supporting reads; the Methods Summary instead mentions ≥1 uniquely aligning read and refers to supplementary frequency cutoffs. (LLM, conf=0.85)

  cites [21] sourceExperimental — accuracy not yet measured

In the paper

“Notably, substitutions, indels, splicing mutations, and gross deletions account for the vast majority (96%) of annotated mutations (27).”

What the sources say

• Supported

  Table 1 (Correspondence; no page indicated) lists 48,343 missense or nonsense substitutions, 8,219 splicing mutations, 13,628 small deletions, 5,567 small insertions, 1,244 small indels, and 5,158 large deletions in HGMD Professional. Together these are 82,159 of its 85,558 entries, or approximately 96%, as of 1 December 2008. (LLM, conf=0.94)

  cites [27] source

In the paper

“Preliminary experiments suggested that existing protocols for Agilent SureSelect hybrid capture (15) and RainDance microdroplet polymerase chain reaction (PCR) (16) but not Febit HybSelect microarray-based biochip capture (30) or Olink padlock probe ligation and PCR (31) yielded consistent target enrichment.”

What the sources say

• Supported

  Citation (15) is attached to Agilent hybrid capture, not to the RainDance, Febit, or Olink methods. The Results section (“Hybrid selection method”) describes capture using Agilent-synthesized oligonucleotides, and “Reproducibility” reports closely matching coverage across independent selections. The preliminary experiments are the citing authors’ own framing. (LLM, conf=0.87)

  cites [15] source
• Supported

  Citation 16 is attached to the RainDance microdroplet PCR protocol, not to the other named methods or the citing authors’ preliminary experiments. The Online Methods identify RainDance equipment in the microdroplet workflow, and the Discussion reports highly reproducible amplification and efficient enrichment of targeted sequences (page not available in our copy). (LLM, conf=0.92)

  cites [16] source
• Partly supported

  The Microarray design and synthesis section (p. 2) identifies a febit Geniom microfluidic array, and Figure 1 (p. 3) describes probes capturing PCR products for detection. The paper does not identify this method as HybSelect or assess whether it yielded consistent target enrichment in the citing authors’ preliminary experiments. (LLM, conf=0.82)

  cites [30] sourceExperimental — accuracy not yet measured

In the paper

“Given that the Human Gene Mutation Database (HGMD) lists 102,433 disease mutations (27), a number that is steadily increasing, a fixed-content method appeared impractical.”

What the sources say

• Partly supported

  The Correspondence section says HGMD records disease-causing mutations and that its annual number of new entries has been steadily increasing. Our copy does not report the claimed total of 102,433 disease mutations; the exact figure is therefore unsupported by this citation. (LLM, conf=0.88)

  cites [27] sourceExperimental — accuracy not yet measured

In the paper

“Previous studies have identified CNVs on the basis of changes in regional coverage along a chromosome in an individual sample (20, 21).”

What the sources say

• Supported

  The CNV-detection discussion reports reduced sequencing coverage for deletions in the AK1 individual genome, and Figure 2 describes a coverage drop defining a deletion. It also reports that increased regional coverage confirmed copy-number gains. The paper used additional evidence alongside coverage, but the claim does not say coverage was the sole basis for detection. (LLM, conf=0.88)

  cites [20] source
• Partly supported

  The Online Methods section on array-based genotyping and CNV detection (page unavailable) confirms that the study identified CNVs in individual DNA samples. It says detection used changes in array-probe intensity and SNP allele ratios, not regional sequencing coverage along a chromosome; that specific method is not supported. (LLM, conf=0.83)

  cites [21] sourceExperimental — accuracy not yet measured

In the paper

“At high volume, the overall analytical cost of the hybrid enrichment-based test was $378, achieving the requirement of <$1 per test per condition and approximating that expended on treatment of severe recessive childhood disorders per U.S. live birth (14, 29).”

What the sources say

• Partly supported

  The screening-test criteria section specifies a cost criterion of less than $1 per infant screened, and the changing technological landscape section says multiplex testing can reduce cost per condition. Neither section establishes a less-than-$1-per-condition requirement or shows that a $378 hybrid enrichment-based test meets it. The copy also does not give the $378 figure or the claimed comparison with treatment expenditure per U.S. live birth. (LLM, conf=0.88)

  cites [14] sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [29] source

In the paper

“Alternatively, microdroplet PCR should theoretically achieve a sensitivity of ~99%, albeit at higher cost (16, 47).”

What the sources say

• Partly supported

  The Discussion reports that more than 99.6% of amplicons were successfully amplified, which supports a roughly 99% figure for amplification success, not necessarily sensitivity. It separately reports a 94.5% variant-detection rate for microdroplet PCR. Our copy does not establish the claimed higher cost relative to an alternative. (LLM, conf=0.86)

  cites [16] sourceExperimental — accuracy not yet measured
• Partly supported

  The Discussion (page unavailable) reports correct variant calls at up to 99.5% of uniquely mappable positions in the targeted regions, supporting a near-99% figure for this method. It does not describe that figure as a theoretical sensitivity or state that microdroplet PCR costs more; searches for sensitivity and cost found no such comparison. (LLM, conf=0.86)

  cites [47] sourceExperimental — accuracy not yet measured

In the paper

“Twenty-six samples were well characterized, from “normal” individuals, and two had previously undergone genome sequencing (21).”

What the sources say

• ?Could not verify

  The Main section reports whole-genome sequencing of two twins in this study, but does not say they were previously genome-sequenced members of a 104-sample set. Searches for the 104 samples and 26 well-characterized normal individuals found no passage addressing those details in our copy. (LLM, conf=0.76)

  cites [21] sourceExperimental — accuracy not yet measured

In the paper

“The distribution of mutations among sequenced samples appeared random.”

In the paper

“At a resultant 160× average target coverage, 93% of nucleotides had at least 20× coverage”

In the paper

“First, with the Illumina HiSeq SBS platform, we used the novel approach of read pair assembly before alignment (99% efficiency) to generate longer reads with high-quality scores (148.6 ± 3.8 nt combined read length and increase in nucleotides with quality score >30 from 75 to 83%).”

In the paper

“As sequence depth increased from 0.7 to 2.7 Gb, sensitivity increased from 93.9 to 95.6%, whereas PPV remained ~100% (Fig. 6A).”

In the paper

“The aligned sequence coverage distribution was unimodal but flat (platykurtic) and right-skewed (Fig. 2B).”

In the paper

“The requirement for ≥14% of reads to call a variant was highly effective for nucleotides with very high coverage and was derived from the genotype data discussed below.”

In the paper

“The positive predictive value (PPV) of sequence-based SNP genotypes was 99.96% and negative predictive value (NPV) was 98.5%, as ascertained by array hybridization.”

In the paper

“Targets with low (<3×) coverage were highly reproducible and had high GC content (table S6).”

In the paper

“This resulted in linear amplification of a subset of targets, ~5% of target nucleotides with zero coverage and a similar proportion of nucleotides on target to that obtained in the best hybrid capture experiments (~30%; Table 1).”

In the paper

“For known substitution, indel, splicing, gross deletion, and regulatory alleles in 76 samples, sensitivity was 100% (113 of 113 known alleles; table S7).”

In the paper

“Interference of bar code nucleotides with hybrid selection did not occur appreciably: The stoichiometry of multiplexed pools was essentially unchanged before and after hybrid selection.”

In the paper

“In practice, the coverage distribution was narrower than hybrid capture but with similar right skewing (Fig. 2D).”

In the paper

“For heterozygote detection, for example, this was equivalent to ~20× coverage, which was achieved in ~96% of exons with ~2.6 gigabases (Gb) of sequence (Fig. 2C).”

In the paper

“This was achieved with hybrid capture after one round of bait redesign for underrepresented exons and decreased bait representation in over-represented exons (Table 1).”

In the paper

“With these cutoffs and a requirement for 20× coverage and 10 reads of quality ≥20 to call a variant, the accuracy of sequence-based SNP genotyping was 98.8%, sensitivity was 94.9%, and specificity was 99.99%.”

In the paper

“NA02057, from a female with aspartylglucosaminuria (OMIM #208400), characterized as a compound heterozygote, was homozygous for two adjacent substitutions (AGA exon 4, c.482G>A, R161Q, chr4:178596918G>A and exon 4, c.488G>C, C163S, chr4:178596912G>C in 38 of 39 reads; Fig. 8), of which C163S had been shown to be the disease mutation (43).”

What the sources say

• ?Not checked — no full text of the sourcecites [43] source

In the paper

“As expected, median coverage increased linearly with sequence depth.”

In the paper

“The proportion of bases with greater than zero and >20× coverage increased toward asymptotes at ~99 and ~96%, respectively (Table 1 and Fig. 2C).”

In the paper

“However, whereas group sizes were small, no significant differences in total carrier burden were found between Caucasians and other ethnicities, between males and females, nor between affected and unaffected individuals (after correction for compound heterozygosity in those affected).”

In the paper

“The requirement for at least 10 high-quality reads to substantiate a variant call resulted in a specificity of 99.96% for single-nucleotide substitutions (which is the limit of accuracy for the gold standard method used) and 100% for about 200 known mutations and new indels in our screening method.”

In the paper

“Four hundred and thirty-seven genes, representing 507 recessive diseases, met these criteria, of which 448 diseases were severe (table S3).”

In the paper

“Specifically, current reference resources contain common polymorphisms that are annotated as disease mutations and erroneous disease mutations.”

In the paper

“Seventy-four percent of these, however, were accounted for by 47 substitutions each with an incidence of ≥5%, of which 20 were homozygous in samples unaffected by the corresponding disease (table S8).”

• Also stated in: § DISCUSSION · plain

  “Unexpectedly, we found that 74% of “disease mutation” calls were accounted for by substitutions with incidences of ≥5%, of which almost one-half were homozygous in samples unaffected by the corresponding disease.”

In the paper

“The burden of nonconservative, nonsynonymous, uncommon (<5% incidence) VUS was ~11 per sample.”

In the paper

“Specificity was 99.96%, and a sensitivity of ~95% was attained with hybrid capture at a sequence depth of 2.5 Gb per sample.”

In the paper

“Second, comprehensive mutation sets, allele frequencies in populations, and individual mutation genotype-phenotype relationships have been defined in very few recessive diseases.”

In the paper

“Of 7028 disorders with suspected Mendelian inheritance, 1139 are recessive and have an established molecular basis.”

• Also stated in: § INTRODUCTION · plain

  “Over the past 25 years, 1139 genes that cause Mendelian recessive diseases have been identified (8).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [8]

In the paper

“Although individual Mendelian diseases are uncommon in general populations, collectively, they account for ~20% of infant mortality and ~10% of pediatric hospitalizations (6, 7).”

What the sources say

• ?Not checked — no full text of the sourcecites [6] source
• ?Not checked — no full text of the sourcecites [7] source

In the paper

“A recent workshop provided recommendations for qualification of new methodologies for broader population-based carrier screening (23). These were high analytical validity, concordance in many settings, high throughput, and cost-effectiveness (including sample acquisition and preparation).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [23]

In the paper

“Preconception screening, together with genetic counseling of carriers, has resulted in remarkable declines in the incidence of several severe recessive diseases including Tay-Sachs disease and cystic fibrosis.”

In the paper

“Note that these genes, although a good representative set, require further assessment of clinical readiness before translation into clinical testing.”

In the paper

“However, extension of preconception screening to most severe disease genes has hitherto been impractical.”

In the paper

“In particular, the accuracy of disease mutation genotypes derived from NGS of enriched targets has been uncertain.”

In the paper

“The proportion of targets with at least 20× coverage appeared to be useful for quality assessment.”

In the paper

“Multiplexing of samples during hybrid selection and NGS had not previously been reported.”

In the paper

“The number of mismatches tolerated for unique alignment of short-read sequences is highly constrained but increases with read length.”

In the paper

“However, comprehensive carrier testing also requires detection of polynucleotide indels, gross insertions, gross deletions, and complex rearrangements.”

In the paper

“Other concerns with array-based screening for recessive disorders were type 1 errors in the absence of confirmatory testing and type 2 errors for disease mutations other than substitutions (complex rearrangements, indels, or gross deletions with uncertain boundaries).”

In the paper

“The vast majority of disease mutations are single-nucleotide substitutions or small indels.”

In the paper

“Third, gross deletions were detected both by perfect alignment to mutant junction reference sequences and by local decreases in normalized coverage (normalized to total sequence generated; C. H. Hu, personal communication).”

In the paper

“Omission of gel purification was critical for scalability of library generation.”

In the paper

“Unambiguous alignment of short-read sequences is typically confounded by repetitive sequences, but was not relevant for carrier testing, because targets overwhelmingly contained unique sequences.”

In the paper

“Of these, the Illumina sequencing-by-synthesis (SBS) and SOLiD sequencing-by-ligation (SBL) platforms are widely disseminated and have throughput of at least 50 Gb per run and read lengths of at least 50 nt.”

In the paper

“This suggested that targets failing hybrid capture could be predicted and, perhaps, rescued by individual PCRs.”

In the paper

“Nevertheless, a burden of 2.8 per genome agreed with theoretical estimates of reproductive lethal allele burden (56).”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [56]

In the paper

“For example, comprehensive newborn screening for treatable or preventable Mendelian diseases would allow early diagnosis and institution of treatment while neonates are asymptomatic.”

In the paper

“Third, many individuals in our cohort were affected by one of these diseases. Although a correction was made for compound heterozygote and homozygote alleles, the burden estimate did not correct for other potential selection biases.”

In the paper

“Community-based carrier testing has had high uptake, without apparent stigma or discrimination and with substantial reductions in the frequencies of tested disorders (3, 48, 49, 51–54).”

What the sources say

• ?Not checked — no full text of the sourcecites [3]
• ?Not checked — no full text of the sourcecites [48] source
• ?Not checked — no full text of the sourcecites [49] source
• ?Not checked — no full text of the sourcecites [51]
• ?Not checked — no full text of the sourcecites [52] source
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [53]
• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [54]

In the paper

“Combining this technology with genetic counseling could reduce the incidence of severe recessive pediatric diseases and may help to expedite diagnosis of these disorders in newborns.”

In the paper

“Finally, the technology platform described herein is agnostic with regard to target genes or clinical setting.”

In the paper

“We noted, however, that identification of larger polynucleotide indels was influenced in some sequences by the particular alignment seed, suggesting that additional refinement of alignment parameters is needed.”

In the paper

“Early treatment can have a profound impact on the clinical severity of conditions and could provide a framework for centralized assessment of investigational new treatments before organ failure.”

In the paper

“Key advantages of NGS are clonal derivation (facilitating unambiguous detection of heterozygous and indel variants), maintenance of phase information (allowing haplotype derivation for adjacent variants), and highly redundant coverage (resulting in extremely low consensus error rates).”

In the paper

“Although the analytical cost will decrease as the throughput of NGS improves, test interpretation, reporting, genetic counseling, and stewardship of mutation databases will confer considerable additional costs.”

In the paper

“In some cases, such as Duarte variant galactosemia, molecular testing would be superior to conventional biochemical testing.”

In the paper

“However, the current study used DNA from Epstein-Barr virus (EBV)–transformed cell lines in which somatic hypermutation has been noted (45).”

What the sources say

• ?Not checked — no full text of the sourcecites [45] source

In the paper

“A variety of medical applications for this technology exist beyond use in preconception carrier screening.”

In the paper

“First, as discussed, an adequate compilation of pathogenic mutations does not currently exist, and strong evidence of pathogenicity was absent for some of the variants referred to as disease mutations.”

In the paper

“As exemplified by cystic fibrosis, the carrier incidence and mutation spectrum of individual recessive disorders vary widely among populations (46).”

What the sources say

• ?Not checked — no full text of the sourcecites [46] source

In the paper

“Adequacy of hierarchical clustering was attested to by samples from identical twins being nearest neighbors, as were two disease mutations in linkage disequilibrium.”

In the paper

“Organ or symptom menu-based diagnostic testing, with masking of nonselected conditions, is anticipated to assist clinical geneticists and pediatric neurologists, because current practice often involves costly, sequential testing of numerous candidate genes.”

In the paper

“Although technical standards and guidelines have been established for laboratory-developed genetic testing for rare disorders in accredited laboratories (26), there are several challenges in their adoption for NGS and bioinformatic-based testing of ~500 conditions.”

What the sources say

• ?Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  cites [26]