Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populations.

Genetic studies in underrepresented populations identify disproportionate numbers of novel associations. However, most genetic studies use genotyping arrays and sequenced reference panels that best capture variation most common in European ancestry populations. To compare data generation strategies best suited for underrepresented populations, we sequenced the whole genomes of 91 individuals to high coverage as part of the Neuropsychiatric Genetics of African Population-Psychosis (NeuroGAP-Psychosis) study with participants from Ethiopia, Kenya, South Africa, and Uganda. We used a downsampling approach to evaluate the quality of two cost-effective data generation strategies, GWAS arrays versus low-coverage sequencing, by calculating the concordance of imputed variants from these technologies with those from deep whole-genome sequencing data. We show that low-coverage sequencing at a depth of ≥4× captures variants of all frequencies more accurately than all commonly used GWAS arrays investigated and at a comparable cost. Lower depths of sequencing (0.5-1×) performed comparably to commonly used low-density GWAS arrays. Low-coverage sequencing is also sensitive to novel variation; 4× sequencing detects 45% of singletons and 95% of common variants identified in high-coverage African whole genomes. Low-coverage sequencing approaches surmount the problems induced by the ascertainment of common genotyping arrays, effectively identify novel variation particularly in underrepresented populations, and present opportunities to enhance variant discovery at a cost similar to traditional approaches.

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms.

BACKGROUND: Here we present an in-depth characterization of the mechanism of sequencer-induced sample contamination due to the phenomenon of index swapping that impacts Illumina sequencers employing patterned flow cells with Exclusion Amplification (ExAmp) chemistry (HiSeqX, HiSeq4000, and NovaSeq). We also present a remediation method that minimizes the impact of such swaps. RESULTS: Leveraging data collected over a two-year period, we demonstrate the widespread prevalence of index swapping in patterned flow cell data. We calculate mean swap rates across multiple sample preparation methods and sequencer models, demonstrating that different library methods can have vastly different swapping rates and that even non-ExAmp chemistry instruments display trace levels of index swapping. We provide methods for eliminating sample data cross contamination by utilizing non-redundant dual indexing for complete filtering of index swapped reads, and share the sequences for 96 non-combinatorial dual indexes we have validated across various library preparation methods and sequencer models. Finally, using computational methods we provide a greater insight into the mechanism of index swapping. CONCLUSIONS: Index swapping in pooled libraries is a prevalent phenomenon that we observe at a rate of 0.2 to 6% in all sequencing runs on HiSeqX, HiSeq 4000/3000, and NovaSeq. Utilizing non-redundant dual indexing allows for the removal (flagging/filtering) of these swapped reads and eliminates swapping induced sample contamination, which is critical for sensitive applications such as RNA-seq, single cell, blood biopsy using circulating tumor DNA, or clinical sequencing.

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.

The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May-July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak.

Beyond asking: Exploring the use of automatic price evaluations to implicitly estimate consumers' willingness-to-pay.

Explicit consumers responses are often adverse for the validity of procedures used to estimate consumers' willingness-to-pay (WTP). This paper investigates if price evaluations occur automatically and to what extent these automatic processes can be used to implicitly estimate consumers' WTP. An adapted version of the task-rule congruency (TRC) paradigm was used in two studies. Results of the first study provided evidence for the notion that prices are automatically evaluated. However, the used procedure had limitations that restricted its utility as an implicit WTP estimate. The procedure was adjusted, and an additional study was conducted. The results of the second study also indicated that prices were evaluated automatically. Additionally, the procedure used during the second study allowed to explore to what extent the observed TRC effects could be used to implicitly estimate consumers' WTP. Taken together, these studies provided evidence for the notion that prices are evaluated automatically. Furthermore, the procedure has the potential to be further developed into an implicit estimate of consumers' WTP.

The frequency effect in second-language visual word recognition.

A lexical decision experiment with Dutch-English bilinguals compared the effect of word frequency on visual word recognition in the first language with that in the second language. Bilinguals showed a considerably larger frequency effect in their second language, even though corpus frequency was matched across languages. Experiment 2 tested monolingual, native speakers of English on the English materials from Experiment 1. This yielded a frequency effect comparable to that of the bilinguals in Dutch (their L1). These results constrain the way in which existing models of word recognition can be extended to unbalanced bilingualism. In particular, the results are compatible with a theory by which the frequency effect originates from implicit learning. They are also compatible with models that attribute frequency effects to serial search in frequency-ordered bins (Murray & Forster, 2004), if these models are extended with the assumption that scanning speed is language dependent, or that bins are not language specific.

The role of executive control in resolving grammatical number conflict in sentence comprehension.

In sentences with a complex subject noun phrase, like "The key to the cabinets is lost", the grammatical number of the head noun (key) may be the same or different from that of the modifier noun phrase (cabinets). When the number is the same, comprehension is usually easier than when it is different. Grammatical number computation may occur while processing the modifier noun (integration phase) or while processing the verb (checking phase). We investigated at which phase number conflict and plausibility of the modifier noun as subject for the verb affect processing, and we imposed a gaze-contingent tone discrimination task in either phase to test whether number computation involves executive control. At both phases, gaze durations were longer when a concurrent tone task was present. Additionally, at the integration phase, gaze durations were longer under number conflict, and this effect was enhanced by the presence of a tone task, whereas no effects of plausibility of the modifier were observed. The finding that the effect of number match was larger under load shows that computation of the grammatical number of the complex noun phrase requires executive control in the integration phase, but not in the checking phase.

The role of working memory in syntactic ambiguity resolution: a psychometric approach.

In 2 studies, the authors used a combination of psychometric and experimental techniques to investigate the effects of domain-general and domain-specific working memory factors on offline decisions concerning attachment of an ambiguous relative clause. Both studies used English and Dutch stimuli presented to English- and Dutch-speaking participants, respectively. In Study 1, readers with low working memory spans were less likely to use recency strategies for disambiguation than were readers with high spans. This finding is inconsistent with predictions of locality- and resource-based accounts of attachment. Psychometric analyses showed that both domain-specific (verbal) and domain-general working memory accounted for the effect. Study 2 found support for the hypothesis that segmentation strategies imposed during silent reading can account for the counterintuitive relationship. Results suggest that readers with low spans have a greater tendency to break up large segments of text because of their limited working memory, leading to high attachment of the ambiguous relative clause.

How important are linguistic factors in word skipping during reading?

The probability of skipping a word is influenced by its processing ease. For instance, a word that is predictable from the preceding context is skipped more often than an unpredictable word. A meta-analysis of studies examining this predictability effect reported effect sizes ranging from 0 to 13%, with an average of 8%. One study does not fit within this picture and reported 23% more skipping of Dutch pronouns in sentences in which the pronoun had no disambiguating value (e.g. 'Mary was envious of Helen because she never looked so good') than in sentences where it did have a disambiguating value (e.g. 'Mary was envious of Albert because she never looked so good'). We re-examined this ambiguity in Dutch using a task that more closely resembles normal reading and observed only a 9% difference in skipping of the pronoun, bringing this linguistic effect in line with the other findings.

Parafoveal-on-foveal effects on eye movements in text reading: does an extra space make a difference?

Schiepers proposed that in text reading, the currently fixated word and the next word are processed in parallel but with a time delay of 90 ms per degree of eccentricity. In his model, the benefit of seeing the upcoming word is due to the fact that the parafoveal information from fixation n is combined with the foveal information from fixation n+1 to boost word recognition, at least when the fixation on word n is of an optimal duration (between 210 and 270 ms). We tested this assumption by adding an extra blank space between the foveal and the parafoveal word. According to the model, this should result in a 30 ms longer processing time for the foveal word. However, reading time was shorter for a word followed by a double space than for a word followed by a single space. An effect of parafoveal word length was also observed with a longer word in the parafoveal leading to shorter fixation times on the foveal word. Implications of these low-level parafoveal-on-foveal effects are discussed.

Cross-structural priming: prepositional phrase attachment primes relative clause attachment.

In this paper we show that attachment height (high vs. low attachment) of a modifier to a complex noun phrase (CNP; e.g., "the servant of the actress"), can be primed between dissimilar syntactic structures. In a sentence completion experiment, we found that the attachment height of a prepositional phrase (PP) in the prime sentence primed the attachment height of a relative clause (RC) in the target sentence. This cross-structural priming effect cannot be explained in terms of the priming of specific phrase-structure rules or even sequences of specific phrase-structure rules (Scheepers, 2003), because the attachment of a PP to a CNP is generated by a different phrase-structure rule than the attachment of an RC. However, the present data suggest that the location at which the RC is attached to the CNP is mentally represented, independent of the specific phrase-structure rule that is attached, or by extension, that the abstract hierarchical configuration of the full CNP and the attached RC is represented (Desmet & Declercq, 2006). This is the first demonstration of a cross-structural priming effect that cannot be captured by phrase-structure rules.

Underspecification of syntactic ambiguities: evidence from self-paced reading.

Syntactically ambiguous sentences are sometimes read faster than disambiguated strings. Models of parsing have explained this tendency by appealing either to a race in the construction of alternative structures or to reanalysis. However, it is also possible that readers of ambiguous sentences save time by strategically underspecifying interpretations of ambiguous attachments. In a self-paced reading study, participants viewed sentences with relative clauses that could attach to one of two sites. Type of question was also manipulated between participants in order to test whether goals can influence reading/parsing strategies. The experiment revealed an ambiguity advantage in reading times, but only when participants expected superficial comprehension questions. When participants expected queries about relative clause interpretation, disambiguating regions were inspected with more care, and the ambiguity advantage was attenuated. However, even when participants expected relative clause queries, question-answering times suggested underspecified representations of ambiguous relative clause attachments. The results support the construal and "good-enough" models of parsing.

The influence of referential discourse context on modifier attachment in Dutch.

In an eye-tracking experiment we investigated the influence of referential context on the attachment of a relative clause to two possible hosts (as in "Someone shot the servant of the actress who was on the balcony"). The attachment of the relative clause was disambiguated grammatically at the first word after the onset of the ambiguity in order to investigate immediate effects of discourse. The contexts had been verified in a sentence completion study to make sure that they induced a strong bias toward early or late closure. The results of the reading experiment, however, revealed no significant interaction of referential context with the attachment preference of the relative clause. The only robust and consistent effect we found was a preference for early closure, independent of the preceding context. These data favor accounts positing that referential context does not influence the initial attachment decision, but does play a role in later phases of sentence processing.

The correspondence between sentence production and corpus frequencies in modifier attachment.

We examined the production of relative clauses in sentences with a complex noun phrase containing two possible attachment sites for the relative clause (e.g., "Someone shot the servant of the actress who was on the balcony."). On the basis of two corpus analyses and two sentence continuation tasks, we conclude that much research about this specific syntactic ambiguity has used complex noun phrases that are quite uncommon. These noun phrases involve the relationship between two humans and, at least in Dutch, induce a different attachment preference from noun phrases referring to non-human entities. We provide evidence that the use of this type of complex noun phrase may have distorted the conclusions about the processes underlying relative clause attachment. In addition, it is shown that, notwithstanding some notable differences between sentence production in the continuation task and in coherent text writing, there seems to be a remarkable correspondence between the attachment patterns obtained with both modes of production.

WordGen: a tool for word selection and nonword generation in Dutch, English, German, and French.

WordGen is an easy-to-use program that uses the CELEX and Lexique lexical databases for word selection and nonword generation in Dutch, English, German, and French. Items can be generated in these four languages, specifying any combination of seven linguistic constraints: number of letters, neighborhood size, frequency, summated position-nonspecific bigram frequency, minimum position-nonspecific bigram f requency, position-specific frequency of the initial and final bigram, and orthographic relatedness. The program also has a module to calculate the respective values of these variables for items that have already been constructed, either with the program or taken from earlier studies. Stimulus queries can be entered through WordGen's graphical user interface or by means of batch files. WordGen is especially useful for (1) Dutch and German item generation, because no such stimulus-selection tool exists for these languages, (2) the generation of nonwords for all four languages, because our program has some important advantages over previous nonword generation approaches, and (3) psycholinguistic experiments on bilingualism, because the possibility of using the same tool for different languages increases the cross-linguistic comparability of the generated item lists. WordGen is free and available at http://expsy.ugent.be/wordgen.htm.